> setwd("/home/nathalie/Private/Travail/Enseignements/formationsINRA/biostat-1-initiation/TP") > gene <- read.table("gene.csv", header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE) > diet <- read.table("diet.csv", header=FALSE, sep="", na.strings="NA", dec=".", strip.white=TRUE) > genotype <- read.table("genotype.csv", header=FALSE, sep="", na.strings="NA", dec=".", strip.white=TRUE) > lipid <- read.table("lipid.csv", header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE) > editDataset(gene) > setwd("/home/nathalie/Private/Travail/Enseignements/formationsINRA/biostat-1-initiation/TP") > gene <- read.table("gene.csv", header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE) > diet <- read.table("diet.csv", header=FALSE, sep="", na.strings="NA", dec=".", strip.white=TRUE) > genotype <- read.table("genotype.csv", header=FALSE, sep="", na.strings="NA", dec=".", strip.white=TRUE) > lipid <- read.table("lipid.csv", header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE) > editDataset(gene) > summary(gene) X36b4 ACAT1 ACAT2 ACBP ACC1 ACC2 ACOTH ADISP ADSS1 ALDH3 Min. :-0.5800 Min. :-0.7500 Min. :-1.1000 Min. :-0.6600 Min. :-1.440 Min. :-1.2000 Min. :-1.0600 Min. :-1.0800 Min. :-1.190 Min. :-0.9900 1st Qu.:-0.5025 1st Qu.:-0.6900 1st Qu.:-0.8800 1st Qu.:-0.5025 1st Qu.:-1.300 1st Qu.:-1.0900 1st Qu.:-0.9500 1st Qu.:-1.0200 1st Qu.:-1.140 1st Qu.:-0.9100 Median :-0.4600 Median :-0.6600 Median :-0.7950 Median :-0.4250 Median :-1.260 Median :-1.0450 Median :-0.9200 Median :-0.9700 Median :-1.075 Median :-0.7850 Mean :-0.4552 Mean :-0.6552 Mean :-0.7668 Mean :-0.4338 Mean :-1.258 Mean :-1.0280 Mean :-0.9107 Mean :-0.9782 Mean :-1.076 Mean :-0.8100 3rd Qu.:-0.4200 3rd Qu.:-0.6200 3rd Qu.:-0.6450 3rd Qu.:-0.3550 3rd Qu.:-1.220 3rd Qu.:-0.9875 3rd Qu.:-0.8800 3rd Qu.:-0.9400 3rd Qu.:-1.035 3rd Qu.:-0.7475 Max. :-0.3000 Max. :-0.5200 Max. :-0.3900 Max. :-0.2400 Max. :-1.070 Max. :-0.7900 Max. :-0.7300 Max. :-0.8700 Max. :-0.910 Max. :-0.6200 AM2R AOX BACT BIEN BSEP Bcl.3 C16SR CACP CAR1 CBS Min. :-0.780 Min. :-0.4800 Min. :-0.4400 Min. :-1.1600 Min. :-0.9000 Min. :-1.220 Min. :1.550 Min. :-1.2600 Min. :-1.1900 Min. :-0.5600 1st Qu.:-0.670 1st Qu.:-0.3175 1st Qu.:-0.3225 1st Qu.:-0.9900 1st Qu.:-0.7600 1st Qu.:-1.103 1st Qu.:1.590 1st Qu.:-1.0325 1st Qu.:-0.9900 1st Qu.:-0.4450 Median :-0.630 Median :-0.2300 Median :-0.3000 Median :-0.9200 Median :-0.7000 Median :-1.065 Median :1.610 Median :-0.9800 Median :-0.9100 Median :-0.4000 Mean :-0.628 Mean :-0.2505 Mean :-0.2828 Mean :-0.9213 Mean :-0.6910 Mean :-1.059 Mean :1.627 Mean :-0.9845 Mean :-0.9135 Mean :-0.3995 3rd Qu.:-0.590 3rd Qu.:-0.1675 3rd Qu.:-0.2350 3rd Qu.:-0.8550 3rd Qu.:-0.6275 3rd Qu.:-1.010 3rd Qu.:1.653 3rd Qu.:-0.9375 3rd Qu.:-0.8475 3rd Qu.:-0.3375 Max. :-0.460 Max. :-0.0400 Max. :-0.1100 Max. :-0.6400 Max. :-0.5100 Max. :-0.910 Max. :1.780 Max. :-0.8300 Max. :-0.6300 Max. :-0.2600 CIDEA COX1 COX2 CPT2 CYP24 CYP26 CYP27a1 CYP27b1 CYP2b10 CYP2b13 Min. :-1.330 Min. :-1.180 Min. :-1.280 Min. :-1.2000 Min. :-1.370 Min. :-1.320 Min. :-0.8800 Min. :-1.350 Min. :-1.320 Min. :-1.370 1st Qu.:-1.232 1st Qu.:-1.093 1st Qu.:-1.180 1st Qu.:-1.0100 1st Qu.:-1.260 1st Qu.:-1.222 1st Qu.:-0.7850 1st Qu.:-1.245 1st Qu.:-1.230 1st Qu.:-1.192 Median :-1.170 Median :-1.055 Median :-1.130 Median :-0.9450 Median :-1.180 Median :-1.150 Median :-0.7300 Median :-1.180 Median :-1.200 Median :-1.140 Mean :-1.184 Mean :-1.050 Mean :-1.135 Mean :-0.9565 Mean :-1.192 Mean :-1.156 Mean :-0.7272 Mean :-1.200 Mean :-1.185 Mean :-1.146 3rd Qu.:-1.140 3rd Qu.:-1.010 3rd Qu.:-1.090 3rd Qu.:-0.8800 3rd Qu.:-1.137 3rd Qu.:-1.100 3rd Qu.:-0.6700 3rd Qu.:-1.150 3rd Qu.:-1.150 3rd Qu.:-1.097 Max. :-1.070 Max. :-0.880 Max. :-1.040 Max. :-0.8200 Max. :-1.050 Max. :-0.960 Max. :-0.5900 Max. :-0.990 Max. :-1.040 Max. :-0.960 CYP2c29 CYP3A11 CYP4A10 CYP4A14 CYP7a CYP8b1 FAS FAT FDFT FXR Min. :-0.5200 Min. :-1.0200 Min. :-1.3300 Min. :-1.2900 Min. :-0.9300 Min. :-1.0100 Min. :-1.0500 Min. :-1.0900 Min. :-1.1700 Min. :-1.0600 1st Qu.:-0.2825 1st Qu.:-0.7125 1st Qu.:-1.1525 1st Qu.:-1.1500 1st Qu.:-0.8000 1st Qu.:-0.7600 1st Qu.:-0.6700 1st Qu.:-1.0400 1st Qu.:-1.0200 1st Qu.:-0.9525 Median :-0.1400 Median :-0.5300 Median :-1.0500 Median :-1.0800 Median :-0.7700 Median :-0.6700 Median :-0.4900 Median :-0.9950 Median :-0.9900 Median :-0.9000 Mean :-0.1472 Mean :-0.5082 Mean :-0.9798 Mean :-0.9930 Mean :-0.7695 Mean :-0.6823 Mean :-0.4517 Mean :-0.9910 Mean :-0.9808 Mean :-0.9105 3rd Qu.:-0.0300 3rd Qu.:-0.3850 3rd Qu.:-0.8175 3rd Qu.:-0.8925 3rd Qu.:-0.7400 3rd Qu.:-0.5900 3rd Qu.:-0.2250 3rd Qu.:-0.9475 3rd Qu.:-0.9375 3rd Qu.:-0.8775 Max. : 0.1800 Max. : 0.0600 Max. :-0.4800 Max. :-0.1500 Max. :-0.6100 Max. :-0.5000 Max. : 0.1800 Max. :-0.7500 Max. :-0.8100 Max. :-0.7600 G6PDH G6Pase GK GS GSTa GSTmu GSTpi2 HMGCoAred HPNCL IL.2 Min. :-1.300 Min. :-1.0600 Min. :-0.9600 Min. :-1.380 Min. :-0.4300 Min. :-0.440 Min. :0.0000 Min. :-1.0700 Min. :-0.9700 Min. :-1.1600 1st Qu.:-1.202 1st Qu.:-0.8200 1st Qu.:-0.8000 1st Qu.:-1.302 1st Qu.:-0.1525 1st Qu.:-0.200 1st Qu.:0.1200 1st Qu.:-0.9700 1st Qu.:-0.7500 1st Qu.:-1.0025 Median :-1.150 Median :-0.6900 Median :-0.7000 Median :-1.225 Median :-0.0900 Median :-0.140 Median :0.2100 Median :-0.9300 Median :-0.6900 Median :-0.9450 Mean :-1.151 Mean :-0.6983 Mean :-0.7145 Mean :-1.232 Mean :-0.1030 Mean :-0.119 Mean :0.2298 Mean :-0.9135 Mean :-0.6937 Mean :-0.9505 3rd Qu.:-1.107 3rd Qu.:-0.5350 3rd Qu.:-0.6200 3rd Qu.:-1.167 3rd Qu.:-0.0350 3rd Qu.:-0.050 3rd Qu.:0.3325 3rd Qu.:-0.8750 3rd Qu.:-0.6075 3rd Qu.:-0.8975 Max. :-0.960 Max. :-0.3800 Max. :-0.4600 Max. :-1.120 Max. : 0.0400 Max. : 0.230 Max. :0.5500 Max. :-0.7000 Max. :-0.5300 Max. :-0.8200 L.FABP LCE LDLr LPK LPL LXRa LXRb Lpin Lpin1 Lpin2 Min. :-0.4600 Min. :-0.26000 Min. :-0.9600 Min. :-0.570 Min. :-1.1100 Min. :-0.9100 Min. :-1.1600 Min. :-1.1300 Min. :-1.1000 Min. :-1.140 1st Qu.:-0.0750 1st Qu.:-0.10000 1st Qu.:-0.8525 1st Qu.:-0.395 1st Qu.:-1.0300 1st Qu.:-0.8400 1st Qu.:-1.0225 1st Qu.:-0.8550 1st Qu.:-0.8700 1st Qu.:-0.910 Median : 0.0600 Median :-0.06000 Median :-0.8200 Median :-0.350 Median :-0.9900 Median :-0.8150 Median :-0.9900 Median :-0.7250 Median :-0.7600 Median :-0.855 Mean : 0.0340 Mean :-0.05275 Mean :-0.8195 Mean :-0.344 Mean :-0.9908 Mean :-0.8115 Mean :-0.9960 Mean :-0.7532 Mean :-0.7648 Mean :-0.849 3rd Qu.: 0.1825 3rd Qu.: 0.00000 3rd Qu.:-0.7675 3rd Qu.:-0.295 3rd Qu.:-0.9500 3rd Qu.:-0.7775 3rd Qu.:-0.9675 3rd Qu.:-0.6150 3rd Qu.:-0.6400 3rd Qu.:-0.775 Max. : 0.2800 Max. : 0.12000 Max. :-0.6800 Max. :-0.130 Max. :-0.8600 Max. :-0.6500 Max. :-0.8400 Max. :-0.4800 Max. :-0.4900 Max. :-0.670 Lpin3 M.CPT1 MCAD MDR1 MDR2 MRP6 MS MTHFR NGFiB NURR1 Min. :-1.290 Min. :-1.290 Min. :-0.7300 Min. :-1.300 Min. :-0.9200 Min. :-1.0900 Min. :-1.200 Min. :-1.100 Min. :-1.290 Min. :-1.320 1st Qu.:-1.198 1st Qu.:-1.165 1st Qu.:-0.6600 1st Qu.:-1.163 1st Qu.:-0.8300 1st Qu.:-1.0025 1st Qu.:-1.110 1st Qu.:-1.002 1st Qu.:-1.200 1st Qu.:-1.210 Median :-1.145 Median :-1.120 Median :-0.6200 Median :-1.120 Median :-0.7800 Median :-0.9550 Median :-1.065 Median :-0.970 Median :-1.120 Median :-1.140 Mean :-1.147 Mean :-1.126 Mean :-0.6050 Mean :-1.134 Mean :-0.7788 Mean :-0.9477 Mean :-1.061 Mean :-0.972 Mean :-1.129 Mean :-1.161 3rd Qu.:-1.097 3rd Qu.:-1.090 3rd Qu.:-0.5575 3rd Qu.:-1.090 3rd Qu.:-0.7175 3rd Qu.:-0.8775 3rd Qu.:-1.008 3rd Qu.:-0.930 3rd Qu.:-1.077 3rd Qu.:-1.107 Max. :-0.980 Max. :-0.960 Max. :-0.4200 Max. :-0.990 Max. :-0.6500 Max. :-0.8300 Max. :-0.880 Max. :-0.880 Max. :-0.910 Max. :-0.950 Ntcp OCTN2 PAL PDK4 PECI PLTP PMDCI PON PPARa PPARd Min. :-0.6500 Min. :-1.280 Min. :-1.320 Min. :-1.280 Min. :-1.1100 Min. :-1.1500 Min. :-1.0700 Min. :-0.7100 Min. :-1.140 Min. :-1.71 1st Qu.:-0.4925 1st Qu.:-1.190 1st Qu.:-1.255 1st Qu.:-1.173 1st Qu.:-0.9225 1st Qu.:-1.0925 1st Qu.:-0.9425 1st Qu.:-0.6325 1st Qu.:-1.022 1st Qu.:-1.59 Median :-0.4400 Median :-1.150 Median :-1.200 Median :-1.130 Median :-0.8400 Median :-1.0500 Median :-0.7650 Median :-0.5800 Median :-0.950 Median :-1.56 Mean :-0.4370 Mean :-1.139 Mean :-1.145 Mean :-1.135 Mean :-0.8472 Mean :-1.0362 Mean :-0.7672 Mean :-0.5825 Mean :-0.966 Mean :-1.56 3rd Qu.:-0.3675 3rd Qu.:-1.080 3rd Qu.:-1.008 3rd Qu.:-1.080 3rd Qu.:-0.7975 3rd Qu.:-0.9975 3rd Qu.:-0.6000 3rd Qu.:-0.5375 3rd Qu.:-0.900 3rd Qu.:-1.51 Max. :-0.2500 Max. :-1.040 Max. :-0.890 Max. :-1.010 Max. :-0.5800 Max. :-0.8500 Max. :-0.4400 Max. :-0.4500 Max. :-0.830 Max. :-1.43 PPARg PXR Pex11a RARa RARb2 RXRa RXRb2 RXRg1 S14 SHP1 Min. :-1.190 Min. :-1.1300 Min. :-1.2000 Min. :-1.300 Min. :-1.300 Min. :-0.7800 Min. :-1.070 Min. :-1.230 Min. :-1.0500 Min. :-1.2100 1st Qu.:-1.090 1st Qu.:-1.0300 1st Qu.:-1.0500 1st Qu.:-1.183 1st Qu.:-1.190 1st Qu.:-0.6725 1st Qu.:-1.000 1st Qu.:-1.143 1st Qu.:-0.9800 1st Qu.:-1.0750 Median :-1.055 Median :-0.9900 Median :-1.0200 Median :-1.130 Median :-1.135 Median :-0.6350 Median :-0.960 Median :-1.100 Median :-0.8550 Median :-0.9900 Mean :-1.052 Mean :-0.9922 Mean :-1.0220 Mean :-1.133 Mean :-1.145 Mean :-0.6360 Mean :-0.964 Mean :-1.095 Mean :-0.8067 Mean :-1.0068 3rd Qu.:-1.010 3rd Qu.:-0.9475 3rd Qu.:-0.9875 3rd Qu.:-1.075 3rd Qu.:-1.090 3rd Qu.:-0.5875 3rd Qu.:-0.935 3rd Qu.:-1.050 3rd Qu.:-0.6575 3rd Qu.:-0.9475 Max. :-0.900 Max. :-0.8400 Max. :-0.9000 Max. :-0.970 Max. :-0.990 Max. :-0.4900 Max. :-0.780 Max. :-0.900 Max. :-0.2500 Max. :-0.7800 SIAT4c SPI1.1 SR.BI THB THIOL TRa TRb Tpalpha Tpbeta UCP2 Min. :-1.1600 Min. :0.960 Min. :-1.060 Min. :-0.9200 Min. :-0.900 Min. :-1.670 Min. :-1.2200 Min. :-1.0000 Min. :-1.310 Min. :-1.0800 1st Qu.:-0.9900 1st Qu.:1.038 1st Qu.:-0.920 1st Qu.:-0.8500 1st Qu.:-0.590 1st Qu.:-1.510 1st Qu.:-1.1100 1st Qu.:-0.8600 1st Qu.:-1.200 1st Qu.:-1.0025 Median :-0.9600 Median :1.075 Median :-0.830 Median :-0.8200 Median :-0.345 Median :-1.460 Median :-1.0600 Median :-0.8300 Median :-1.140 Median :-0.9800 Mean :-0.9623 Mean :1.091 Mean :-0.843 Mean :-0.8170 Mean :-0.411 Mean :-1.457 Mean :-1.0542 Mean :-0.8183 Mean :-1.130 Mean :-0.9660 3rd Qu.:-0.9275 3rd Qu.:1.150 3rd Qu.:-0.800 3rd Qu.:-0.7875 3rd Qu.:-0.230 3rd Qu.:-1.395 3rd Qu.:-0.9975 3rd Qu.:-0.7600 3rd Qu.:-1.065 3rd Qu.:-0.9275 Max. :-0.8400 Max. :1.230 Max. :-0.610 Max. :-0.6900 Max. :-0.030 Max. :-1.220 Max. :-0.9200 Max. :-0.6500 Max. :-0.910 Max. :-0.7600 UCP3 VDR VLDLr Waf1 ap2 apoA.I apoB apoC3 apoE c.fos cHMGCoAS Min. :-1.270 Min. :-1.300 Min. :-1.190 Min. :-1.300 Min. :-1.370 Min. :0.5400 Min. :-0.2700 Min. :-0.4900 Min. :0.860 Min. :-1.220 Min. :-1.240 1st Qu.:-1.153 1st Qu.:-1.180 1st Qu.:-1.093 1st Qu.:-1.150 1st Qu.:-1.222 1st Qu.:0.6575 1st Qu.:-0.2000 1st Qu.:-0.3900 1st Qu.:0.980 1st Qu.:-1.150 1st Qu.:-1.103 Median :-1.110 Median :-1.120 Median :-1.055 Median :-1.130 Median :-1.190 Median :0.7200 Median :-0.1700 Median :-0.3400 Median :1.040 Median :-1.110 Median :-1.030 Mean :-1.108 Mean :-1.132 Mean :-1.053 Mean :-1.123 Mean :-1.188 Mean :0.7295 Mean :-0.1675 Mean :-0.3407 Mean :1.028 Mean :-1.105 Mean :-1.014 3rd Qu.:-1.050 3rd Qu.:-1.080 3rd Qu.:-1.010 3rd Qu.:-1.087 3rd Qu.:-1.147 3rd Qu.:0.8100 3rd Qu.:-0.1450 3rd Qu.:-0.3000 3rd Qu.:1.070 3rd Qu.:-1.060 3rd Qu.:-0.910 Max. :-0.920 Max. :-0.940 Max. :-0.910 Max. :-0.940 Max. :-1.080 Max. :0.9200 Max. : 0.0100 Max. :-0.1800 Max. :1.180 Max. :-0.980 Max. :-0.780 cMOAT eif2g hABC1 i.BABP i.BAT i.FABP i.NOS mABC1 mHMGCoAS Min. :-1.0200 Min. :-1.230 Min. :-1.250 Min. :-0.8900 Min. :-1.890 Min. :-1.300 Min. :-1.430 Min. :-0.9800 Min. :-0.5800 1st Qu.:-0.8950 1st Qu.:-1.100 1st Qu.:-1.173 1st Qu.:-0.8325 1st Qu.:-1.742 1st Qu.:-1.170 1st Qu.:-1.285 1st Qu.:-0.9200 1st Qu.:-0.3000 Median :-0.8700 Median :-1.055 Median :-1.135 Median :-0.8000 Median :-1.690 Median :-1.140 Median :-1.240 Median :-0.8700 Median :-0.2100 Mean :-0.8485 Mean :-1.058 Mean :-1.138 Mean :-0.7935 Mean :-1.698 Mean :-1.122 Mean :-1.246 Mean :-0.8765 Mean :-0.2210 3rd Qu.:-0.7875 3rd Qu.:-1.020 3rd Qu.:-1.097 3rd Qu.:-0.7475 3rd Qu.:-1.660 3rd Qu.:-1.075 3rd Qu.:-1.208 3rd Qu.:-0.8375 3rd Qu.:-0.1275 Max. :-0.6900 Max. :-0.840 Max. :-0.980 Max. :-0.6700 Max. :-1.550 Max. :-0.930 Max. :-1.090 Max. :-0.8000 Max. : 0.0600 > summary(diet) # after having selected "genes" V1 coc :8 fish:8 lin :8 ref :8 sun :8 > ls() [1] "diet" "gene" "genotype" "lipid" > sapply(gene, function(x)(sum(is.na(x)))) # NA counts X36b4 ACAT1 ACAT2 ACBP ACC1 ACC2 ACOTH ADISP ADSS1 ALDH3 AM2R AOX BACT BIEN BSEP Bcl.3 C16SR CACP 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 CAR1 CBS CIDEA COX1 COX2 CPT2 CYP24 CYP26 CYP27a1 CYP27b1 CYP2b10 CYP2b13 CYP2c29 CYP3A11 CYP4A10 CYP4A14 CYP7a CYP8b1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 FAS FAT FDFT FXR G6PDH G6Pase GK GS GSTa GSTmu GSTpi2 HMGCoAred HPNCL IL.2 L.FABP LCE LDLr LPK 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LPL LXRa LXRb Lpin Lpin1 Lpin2 Lpin3 M.CPT1 MCAD MDR1 MDR2 MRP6 MS MTHFR NGFiB NURR1 Ntcp OCTN2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PAL PDK4 PECI PLTP PMDCI PON PPARa PPARd PPARg PXR Pex11a RARa RARb2 RXRa RXRb2 RXRg1 S14 SHP1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 SIAT4c SPI1.1 SR.BI THB THIOL TRa TRb Tpalpha Tpbeta UCP2 UCP3 VDR VLDLr Waf1 ap2 apoA.I apoB apoC3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 apoE c.fos cHMGCoAS cMOAT eif2g hABC1 i.BABP i.BAT i.FABP i.NOS mABC1 mHMGCoAS 0 0 0 0 0 0 0 0 0 0 0 0 > library(abind, pos=15) > library(e1071, pos=16) > numSummary(lipid[,c("C16.1n.7", "C16.1n.9")], statistics=c("mean", "sd", "IQR", "quantiles", "cv", "skewness", "kurtosis"), quantiles=c(0,.25,.5,.75,1)) mean sd IQR cv skewness kurtosis 0% 25% 50% 75% 100% n C16.1n.7 4.41875 2.9849702 2.320 0.6755237 1.9309189 3.1882201 1.59 2.6325 3.300 4.9525 13.9 40 C16.1n.9 0.68700 0.2849849 0.355 0.4148252 0.9524791 0.5377586 0.29 0.4575 0.645 0.8125 1.5 40 > Boxplot( ~ C16.1n.7, data=lipid, id.method="y") [1] "21" "31" "32" "36" > Boxplot( ~ C16.1n.9, data=lipid, id.method="identify", main="Mon joli graphique") [1] "32" > boxplot(lipid, main = "distribution des lipides") > boxplot(gene) > dev.print(png, filename="boxplots_genes.png", width=13, height=8, pointsize=12, units="in", res=72) X11cairo 2 > X11() > with(lipid, Hist(C16.1n.7, scale="frequency", breaks="Sturges", col="darkgray")) > with(lipid, Hist(C16.1n.9, scale="frequency", breaks="Sturges", col="darkgray")) > with(lipid, Hist(C16.1n.7, scale="frequency", breaks=20, col="darkgray")) > lipid$log.C16.1n.7 <- with(lipid, log(C16.1n.7+1)) > with(lipid, Hist(log.C16.1n.7, scale="frequency", breaks=20, col="darkgray")) > # numerical summaries > numSummary(lipid[,"log.C16.1n.7"], statistics=c("quantiles", "skewness"), quantiles=c(0,.25,.5,.75,1), type="2") skewness 0% 25% 50% 75% 100% n 1.1847 0.9516579 1.289886 1.458591 1.783648 2.701361 40 > lipid <- local({ + .Z <- scale(lipid[,c("C14.0","C16.0","C16.1n.7","C16.1n.9","C18.0","C18.1n.7","C18.1n.9","C18.2n.6","C18.3n.3","C18.3n.6","C20.1n.9","C20.2n.6","C20.3n.3","C20.3n.6", + "C20.3n.9","C20.4n.6","C20.5n.3","C22.4n.6","C22.5n.3","C22.5n.6","C22.6n.3")]) + within(lipid, { + Z.C22.6n.3 <- .Z[,21] + Z.C22.5n.6 <- .Z[,20] + Z.C22.5n.3 <- .Z[,19] + Z.C22.4n.6 <- .Z[,18] + Z.C20.5n.3 <- .Z[,17] + Z.C20.4n.6 <- .Z[,16] + Z.C20.3n.9 <- .Z[,15] + Z.C20.3n.6 <- .Z[,14] + Z.C20.3n.3 <- .Z[,13] + Z.C20.2n.6 <- .Z[,12] + Z.C20.1n.9 <- .Z[,11] + Z.C18.3n.6 <- .Z[,10] + Z.C18.3n.3 <- .Z[,9] + Z.C18.2n.6 <- .Z[,8] + Z.C18.1n.9 <- .Z[,7] + Z.C18.1n.7 <- .Z[,6] + Z.C18.0 <- .Z[,5] + Z.C16.1n.9 <- .Z[,4] + Z.C16.1n.7 <- .Z[,3] + Z.C16.0 <- .Z[,2] + Z.C14.0 <- .Z[,1] + }) + }) > boxplot(lipid) > numSummary(lipid[,c("Z.C14.0", "Z.C16.0", "Z.C16.1n.7", "Z.C16.1n.9", "Z.C18.0", "Z.C18.1n.7", "Z.C18.1n.9", "Z.C18.2n.6", "Z.C18.3n.3", "Z.C18.3n.6", "Z.C20.1n.9", + "Z.C20.2n.6", "Z.C20.3n.3", "Z.C20.3n.6", "Z.C20.3n.9", "Z.C20.4n.6", "Z.C20.5n.3", "Z.C22.4n.6", "Z.C22.5n.3", "Z.C22.5n.6", "Z.C22.6n.3")], statistics=c("mean", "sd"), + quantiles=c(0,.25,.5,.75,1)) mean sd n Z.C14.0 -1.110223e-17 1 40 Z.C16.0 4.336809e-18 1 40 Z.C16.1n.7 -4.857226e-17 1 40 Z.C16.1n.9 -1.724315e-16 1 40 Z.C18.0 7.997075e-17 1 40 Z.C18.1n.7 -2.844947e-17 1 40 Z.C18.1n.9 -1.389514e-16 1 40 Z.C18.2n.6 -1.214306e-18 1 40 Z.C18.3n.3 2.706169e-17 1 40 Z.C18.3n.6 -3.469447e-19 1 40 Z.C20.1n.9 -1.981054e-16 1 40 Z.C20.2n.6 1.474515e-18 1 40 Z.C20.3n.3 4.163336e-17 1 40 Z.C20.3n.6 -3.348016e-17 1 40 Z.C20.3n.9 -3.486794e-17 1 40 Z.C20.4n.6 -4.232725e-17 1 40 Z.C20.5n.3 -3.469447e-17 1 40 Z.C22.4n.6 2.550044e-17 1 40 Z.C22.5n.3 -3.885781e-17 1 40 Z.C22.5n.6 -2.281161e-17 1 40 Z.C22.6n.3 7.671815e-17 1 40 > lipid.Z <- lipid # copy lipid in a new data set: lipid.Z > lipid.Z <- within(lipid.Z, { + C14.0 <- NULL + C16.0 <- NULL + C16.1n.7 <- NULL + C16.1n.9 <- NULL + C18.0 <- NULL + C18.1n.7 <- NULL + C18.1n.9 <- NULL + C18.2n.6 <- NULL + C18.3n.3 <- NULL + C18.3n.6 <- NULL + C20.1n.9 <- NULL + C20.2n.6 <- NULL + C20.3n.3 <- NULL + C20.3n.6 <- NULL + C20.3n.9 <- NULL + C20.4n.6 <- NULL + C20.5n.3 <- NULL + C22.4n.6 <- NULL + C22.5n.3 <- NULL + C22.5n.6 <- NULL + C22.6n.3 <- NULL + log.C16.1n.7 <- NULL + }) > boxplot(lipid.Z) > lipid <- within(lipid, { + Z.C14.0 <- NULL + Z.C16.0 <- NULL + Z.C16.1n.7 <- NULL + Z.C16.1n.9 <- NULL + Z.C18.0 <- NULL + Z.C18.1n.7 <- NULL + Z.C18.1n.9 <- NULL + Z.C18.2n.6 <- NULL + Z.C18.3n.3 <- NULL + Z.C18.3n.6 <- NULL + Z.C20.1n.9 <- NULL + Z.C20.2n.6 <- NULL + Z.C20.3n.3 <- NULL + Z.C20.3n.6 <- NULL + Z.C20.3n.9 <- NULL + Z.C20.4n.6 <- NULL + Z.C20.5n.3 <- NULL + Z.C22.4n.6 <- NULL + Z.C22.5n.3 <- NULL + Z.C22.5n.6 <- NULL + Z.C22.6n.3 <- NULL + }) > local({ + .Table <- with(diet, table(V1)) + cat("\ncounts:\n") + print(.Table) + cat("\npercentages:\n") + print(round(100*.Table/sum(.Table), 2)) + }) counts: V1 coc fish lin ref sun 8 8 8 8 8 percentages: V1 coc fish lin ref sun 20 20 20 20 20 > with(diet, Barplot(V1, xlab="V1", ylab="Frequency")) > library(colorspace, pos=17) > with(diet, pie(table(V1), labels=levels(V1), xlab="", ylab="", main="V1", col=rainbow_hcl(length(levels(V1))))) > total <- merge(diet, gene, all=TRUE, by="row.names") > rownames(total) <- total$Row.names > total$Row.names <- NULL > total <- merge(total, genotype, all=TRUE, by="row.names") > rownames(total) <- total$Row.names > total$Row.names <- NULL > total <- merge(total, lipid, all=TRUE, by="row.names") > rownames(total) <- total$Row.names > total$Row.names <- NULL > summary(total) V1.x X36b4 ACAT1 ACAT2 ACBP ACC1 ACC2 ACOTH ADISP ADSS1 ALDH3 coc :8 Min. :-0.5800 Min. :-0.7500 Min. :-1.1000 Min. :-0.6600 Min. :-1.440 Min. :-1.2000 Min. :-1.0600 Min. :-1.0800 Min. :-1.190 Min. :-0.9900 fish:8 1st Qu.:-0.5025 1st Qu.:-0.6900 1st Qu.:-0.8800 1st Qu.:-0.5025 1st Qu.:-1.300 1st Qu.:-1.0900 1st Qu.:-0.9500 1st Qu.:-1.0200 1st Qu.:-1.140 1st Qu.:-0.9100 lin :8 Median :-0.4600 Median :-0.6600 Median :-0.7950 Median :-0.4250 Median :-1.260 Median :-1.0450 Median :-0.9200 Median :-0.9700 Median :-1.075 Median :-0.7850 ref :8 Mean :-0.4552 Mean :-0.6552 Mean :-0.7668 Mean :-0.4338 Mean :-1.258 Mean :-1.0280 Mean :-0.9107 Mean :-0.9782 Mean :-1.076 Mean :-0.8100 sun :8 3rd Qu.:-0.4200 3rd Qu.:-0.6200 3rd Qu.:-0.6450 3rd Qu.:-0.3550 3rd Qu.:-1.220 3rd Qu.:-0.9875 3rd Qu.:-0.8800 3rd Qu.:-0.9400 3rd Qu.:-1.035 3rd Qu.:-0.7475 Max. :-0.3000 Max. :-0.5200 Max. :-0.3900 Max. :-0.2400 Max. :-1.070 Max. :-0.7900 Max. :-0.7300 Max. :-0.8700 Max. :-0.910 Max. :-0.6200 AM2R AOX BACT BIEN BSEP Bcl.3 C16SR CACP CAR1 CBS Min. :-0.780 Min. :-0.4800 Min. :-0.4400 Min. :-1.1600 Min. :-0.9000 Min. :-1.220 Min. :1.550 Min. :-1.2600 Min. :-1.1900 Min. :-0.5600 1st Qu.:-0.670 1st Qu.:-0.3175 1st Qu.:-0.3225 1st Qu.:-0.9900 1st Qu.:-0.7600 1st Qu.:-1.103 1st Qu.:1.590 1st Qu.:-1.0325 1st Qu.:-0.9900 1st Qu.:-0.4450 Median :-0.630 Median :-0.2300 Median :-0.3000 Median :-0.9200 Median :-0.7000 Median :-1.065 Median :1.610 Median :-0.9800 Median :-0.9100 Median :-0.4000 Mean :-0.628 Mean :-0.2505 Mean :-0.2828 Mean :-0.9213 Mean :-0.6910 Mean :-1.059 Mean :1.627 Mean :-0.9845 Mean :-0.9135 Mean :-0.3995 3rd Qu.:-0.590 3rd Qu.:-0.1675 3rd Qu.:-0.2350 3rd Qu.:-0.8550 3rd Qu.:-0.6275 3rd Qu.:-1.010 3rd Qu.:1.653 3rd Qu.:-0.9375 3rd Qu.:-0.8475 3rd Qu.:-0.3375 Max. :-0.460 Max. :-0.0400 Max. :-0.1100 Max. :-0.6400 Max. :-0.5100 Max. :-0.910 Max. :1.780 Max. :-0.8300 Max. :-0.6300 Max. :-0.2600 CIDEA COX1 COX2 CPT2 CYP24 CYP26 CYP27a1 CYP27b1 CYP2b10 CYP2b13 Min. :-1.330 Min. :-1.180 Min. :-1.280 Min. :-1.2000 Min. :-1.370 Min. :-1.320 Min. :-0.8800 Min. :-1.350 Min. :-1.320 Min. :-1.370 1st Qu.:-1.232 1st Qu.:-1.093 1st Qu.:-1.180 1st Qu.:-1.0100 1st Qu.:-1.260 1st Qu.:-1.222 1st Qu.:-0.7850 1st Qu.:-1.245 1st Qu.:-1.230 1st Qu.:-1.192 Median :-1.170 Median :-1.055 Median :-1.130 Median :-0.9450 Median :-1.180 Median :-1.150 Median :-0.7300 Median :-1.180 Median :-1.200 Median :-1.140 Mean :-1.184 Mean :-1.050 Mean :-1.135 Mean :-0.9565 Mean :-1.192 Mean :-1.156 Mean :-0.7272 Mean :-1.200 Mean :-1.185 Mean :-1.146 3rd Qu.:-1.140 3rd Qu.:-1.010 3rd Qu.:-1.090 3rd Qu.:-0.8800 3rd Qu.:-1.137 3rd Qu.:-1.100 3rd Qu.:-0.6700 3rd Qu.:-1.150 3rd Qu.:-1.150 3rd Qu.:-1.097 Max. :-1.070 Max. :-0.880 Max. :-1.040 Max. :-0.8200 Max. :-1.050 Max. :-0.960 Max. :-0.5900 Max. :-0.990 Max. :-1.040 Max. :-0.960 CYP2c29 CYP3A11 CYP4A10 CYP4A14 CYP7a CYP8b1 FAS FAT FDFT FXR Min. :-0.5200 Min. :-1.0200 Min. :-1.3300 Min. :-1.2900 Min. :-0.9300 Min. :-1.0100 Min. :-1.0500 Min. :-1.0900 Min. :-1.1700 Min. :-1.0600 1st Qu.:-0.2825 1st Qu.:-0.7125 1st Qu.:-1.1525 1st Qu.:-1.1500 1st Qu.:-0.8000 1st Qu.:-0.7600 1st Qu.:-0.6700 1st Qu.:-1.0400 1st Qu.:-1.0200 1st Qu.:-0.9525 Median :-0.1400 Median :-0.5300 Median :-1.0500 Median :-1.0800 Median :-0.7700 Median :-0.6700 Median :-0.4900 Median :-0.9950 Median :-0.9900 Median :-0.9000 Mean :-0.1472 Mean :-0.5082 Mean :-0.9798 Mean :-0.9930 Mean :-0.7695 Mean :-0.6823 Mean :-0.4517 Mean :-0.9910 Mean :-0.9808 Mean :-0.9105 3rd Qu.:-0.0300 3rd Qu.:-0.3850 3rd Qu.:-0.8175 3rd Qu.:-0.8925 3rd Qu.:-0.7400 3rd Qu.:-0.5900 3rd Qu.:-0.2250 3rd Qu.:-0.9475 3rd Qu.:-0.9375 3rd Qu.:-0.8775 Max. : 0.1800 Max. : 0.0600 Max. :-0.4800 Max. :-0.1500 Max. :-0.6100 Max. :-0.5000 Max. : 0.1800 Max. :-0.7500 Max. :-0.8100 Max. :-0.7600 G6PDH G6Pase GK GS GSTa GSTmu GSTpi2 HMGCoAred HPNCL IL.2 Min. :-1.300 Min. :-1.0600 Min. :-0.9600 Min. :-1.380 Min. :-0.4300 Min. :-0.440 Min. :0.0000 Min. :-1.0700 Min. :-0.9700 Min. :-1.1600 1st Qu.:-1.202 1st Qu.:-0.8200 1st Qu.:-0.8000 1st Qu.:-1.302 1st Qu.:-0.1525 1st Qu.:-0.200 1st Qu.:0.1200 1st Qu.:-0.9700 1st Qu.:-0.7500 1st Qu.:-1.0025 Median :-1.150 Median :-0.6900 Median :-0.7000 Median :-1.225 Median :-0.0900 Median :-0.140 Median :0.2100 Median :-0.9300 Median :-0.6900 Median :-0.9450 Mean :-1.151 Mean :-0.6983 Mean :-0.7145 Mean :-1.232 Mean :-0.1030 Mean :-0.119 Mean :0.2298 Mean :-0.9135 Mean :-0.6937 Mean :-0.9505 3rd Qu.:-1.107 3rd Qu.:-0.5350 3rd Qu.:-0.6200 3rd Qu.:-1.167 3rd Qu.:-0.0350 3rd Qu.:-0.050 3rd Qu.:0.3325 3rd Qu.:-0.8750 3rd Qu.:-0.6075 3rd Qu.:-0.8975 Max. :-0.960 Max. :-0.3800 Max. :-0.4600 Max. :-1.120 Max. : 0.0400 Max. : 0.230 Max. :0.5500 Max. :-0.7000 Max. :-0.5300 Max. :-0.8200 L.FABP LCE LDLr LPK LPL LXRa LXRb Lpin Lpin1 Lpin2 Min. :-0.4600 Min. :-0.26000 Min. :-0.9600 Min. :-0.570 Min. :-1.1100 Min. :-0.9100 Min. :-1.1600 Min. :-1.1300 Min. :-1.1000 Min. :-1.140 1st Qu.:-0.0750 1st Qu.:-0.10000 1st Qu.:-0.8525 1st Qu.:-0.395 1st Qu.:-1.0300 1st Qu.:-0.8400 1st Qu.:-1.0225 1st Qu.:-0.8550 1st Qu.:-0.8700 1st Qu.:-0.910 Median : 0.0600 Median :-0.06000 Median :-0.8200 Median :-0.350 Median :-0.9900 Median :-0.8150 Median :-0.9900 Median :-0.7250 Median :-0.7600 Median :-0.855 Mean : 0.0340 Mean :-0.05275 Mean :-0.8195 Mean :-0.344 Mean :-0.9908 Mean :-0.8115 Mean :-0.9960 Mean :-0.7532 Mean :-0.7648 Mean :-0.849 3rd Qu.: 0.1825 3rd Qu.: 0.00000 3rd Qu.:-0.7675 3rd Qu.:-0.295 3rd Qu.:-0.9500 3rd Qu.:-0.7775 3rd Qu.:-0.9675 3rd Qu.:-0.6150 3rd Qu.:-0.6400 3rd Qu.:-0.775 Max. : 0.2800 Max. : 0.12000 Max. :-0.6800 Max. :-0.130 Max. :-0.8600 Max. :-0.6500 Max. :-0.8400 Max. :-0.4800 Max. :-0.4900 Max. :-0.670 Lpin3 M.CPT1 MCAD MDR1 MDR2 MRP6 MS MTHFR NGFiB NURR1 Min. :-1.290 Min. :-1.290 Min. :-0.7300 Min. :-1.300 Min. :-0.9200 Min. :-1.0900 Min. :-1.200 Min. :-1.100 Min. :-1.290 Min. :-1.320 1st Qu.:-1.198 1st Qu.:-1.165 1st Qu.:-0.6600 1st Qu.:-1.163 1st Qu.:-0.8300 1st Qu.:-1.0025 1st Qu.:-1.110 1st Qu.:-1.002 1st Qu.:-1.200 1st Qu.:-1.210 Median :-1.145 Median :-1.120 Median :-0.6200 Median :-1.120 Median :-0.7800 Median :-0.9550 Median :-1.065 Median :-0.970 Median :-1.120 Median :-1.140 Mean :-1.147 Mean :-1.126 Mean :-0.6050 Mean :-1.134 Mean :-0.7788 Mean :-0.9477 Mean :-1.061 Mean :-0.972 Mean :-1.129 Mean :-1.161 3rd Qu.:-1.097 3rd Qu.:-1.090 3rd Qu.:-0.5575 3rd Qu.:-1.090 3rd Qu.:-0.7175 3rd Qu.:-0.8775 3rd Qu.:-1.008 3rd Qu.:-0.930 3rd Qu.:-1.077 3rd Qu.:-1.107 Max. :-0.980 Max. :-0.960 Max. :-0.4200 Max. :-0.990 Max. :-0.6500 Max. :-0.8300 Max. :-0.880 Max. :-0.880 Max. :-0.910 Max. :-0.950 Ntcp OCTN2 PAL PDK4 PECI PLTP PMDCI PON PPARa PPARd Min. :-0.6500 Min. :-1.280 Min. :-1.320 Min. :-1.280 Min. :-1.1100 Min. :-1.1500 Min. :-1.0700 Min. :-0.7100 Min. :-1.140 Min. :-1.71 1st Qu.:-0.4925 1st Qu.:-1.190 1st Qu.:-1.255 1st Qu.:-1.173 1st Qu.:-0.9225 1st Qu.:-1.0925 1st Qu.:-0.9425 1st Qu.:-0.6325 1st Qu.:-1.022 1st Qu.:-1.59 Median :-0.4400 Median :-1.150 Median :-1.200 Median :-1.130 Median :-0.8400 Median :-1.0500 Median :-0.7650 Median :-0.5800 Median :-0.950 Median :-1.56 Mean :-0.4370 Mean :-1.139 Mean :-1.145 Mean :-1.135 Mean :-0.8472 Mean :-1.0362 Mean :-0.7672 Mean :-0.5825 Mean :-0.966 Mean :-1.56 3rd Qu.:-0.3675 3rd Qu.:-1.080 3rd Qu.:-1.008 3rd Qu.:-1.080 3rd Qu.:-0.7975 3rd Qu.:-0.9975 3rd Qu.:-0.6000 3rd Qu.:-0.5375 3rd Qu.:-0.900 3rd Qu.:-1.51 Max. :-0.2500 Max. :-1.040 Max. :-0.890 Max. :-1.010 Max. :-0.5800 Max. :-0.8500 Max. :-0.4400 Max. :-0.4500 Max. :-0.830 Max. :-1.43 PPARg PXR Pex11a RARa RARb2 RXRa RXRb2 RXRg1 S14 SHP1 Min. :-1.190 Min. :-1.1300 Min. :-1.2000 Min. :-1.300 Min. :-1.300 Min. :-0.7800 Min. :-1.070 Min. :-1.230 Min. :-1.0500 Min. :-1.2100 1st Qu.:-1.090 1st Qu.:-1.0300 1st Qu.:-1.0500 1st Qu.:-1.183 1st Qu.:-1.190 1st Qu.:-0.6725 1st Qu.:-1.000 1st Qu.:-1.143 1st Qu.:-0.9800 1st Qu.:-1.0750 Median :-1.055 Median :-0.9900 Median :-1.0200 Median :-1.130 Median :-1.135 Median :-0.6350 Median :-0.960 Median :-1.100 Median :-0.8550 Median :-0.9900 Mean :-1.052 Mean :-0.9922 Mean :-1.0220 Mean :-1.133 Mean :-1.145 Mean :-0.6360 Mean :-0.964 Mean :-1.095 Mean :-0.8067 Mean :-1.0068 3rd Qu.:-1.010 3rd Qu.:-0.9475 3rd Qu.:-0.9875 3rd Qu.:-1.075 3rd Qu.:-1.090 3rd Qu.:-0.5875 3rd Qu.:-0.935 3rd Qu.:-1.050 3rd Qu.:-0.6575 3rd Qu.:-0.9475 Max. :-0.900 Max. :-0.8400 Max. :-0.9000 Max. :-0.970 Max. :-0.990 Max. :-0.4900 Max. :-0.780 Max. :-0.900 Max. :-0.2500 Max. :-0.7800 SIAT4c SPI1.1 SR.BI THB THIOL TRa TRb Tpalpha Tpbeta UCP2 Min. :-1.1600 Min. :0.960 Min. :-1.060 Min. :-0.9200 Min. :-0.900 Min. :-1.670 Min. :-1.2200 Min. :-1.0000 Min. :-1.310 Min. :-1.0800 1st Qu.:-0.9900 1st Qu.:1.038 1st Qu.:-0.920 1st Qu.:-0.8500 1st Qu.:-0.590 1st Qu.:-1.510 1st Qu.:-1.1100 1st Qu.:-0.8600 1st Qu.:-1.200 1st Qu.:-1.0025 Median :-0.9600 Median :1.075 Median :-0.830 Median :-0.8200 Median :-0.345 Median :-1.460 Median :-1.0600 Median :-0.8300 Median :-1.140 Median :-0.9800 Mean :-0.9623 Mean :1.091 Mean :-0.843 Mean :-0.8170 Mean :-0.411 Mean :-1.457 Mean :-1.0542 Mean :-0.8183 Mean :-1.130 Mean :-0.9660 3rd Qu.:-0.9275 3rd Qu.:1.150 3rd Qu.:-0.800 3rd Qu.:-0.7875 3rd Qu.:-0.230 3rd Qu.:-1.395 3rd Qu.:-0.9975 3rd Qu.:-0.7600 3rd Qu.:-1.065 3rd Qu.:-0.9275 Max. :-0.8400 Max. :1.230 Max. :-0.610 Max. :-0.6900 Max. :-0.030 Max. :-1.220 Max. :-0.9200 Max. :-0.6500 Max. :-0.910 Max. :-0.7600 UCP3 VDR VLDLr Waf1 ap2 apoA.I apoB apoC3 apoE c.fos cHMGCoAS Min. :-1.270 Min. :-1.300 Min. :-1.190 Min. :-1.300 Min. :-1.370 Min. :0.5400 Min. :-0.2700 Min. :-0.4900 Min. :0.860 Min. :-1.220 Min. :-1.240 1st Qu.:-1.153 1st Qu.:-1.180 1st Qu.:-1.093 1st Qu.:-1.150 1st Qu.:-1.222 1st Qu.:0.6575 1st Qu.:-0.2000 1st Qu.:-0.3900 1st Qu.:0.980 1st Qu.:-1.150 1st Qu.:-1.103 Median :-1.110 Median :-1.120 Median :-1.055 Median :-1.130 Median :-1.190 Median :0.7200 Median :-0.1700 Median :-0.3400 Median :1.040 Median :-1.110 Median :-1.030 Mean :-1.108 Mean :-1.132 Mean :-1.053 Mean :-1.123 Mean :-1.188 Mean :0.7295 Mean :-0.1675 Mean :-0.3407 Mean :1.028 Mean :-1.105 Mean :-1.014 3rd Qu.:-1.050 3rd Qu.:-1.080 3rd Qu.:-1.010 3rd Qu.:-1.087 3rd Qu.:-1.147 3rd Qu.:0.8100 3rd Qu.:-0.1450 3rd Qu.:-0.3000 3rd Qu.:1.070 3rd Qu.:-1.060 3rd Qu.:-0.910 Max. :-0.920 Max. :-0.940 Max. :-0.910 Max. :-0.940 Max. :-1.080 Max. :0.9200 Max. : 0.0100 Max. :-0.1800 Max. :1.180 Max. :-0.980 Max. :-0.780 cMOAT eif2g hABC1 i.BABP i.BAT i.FABP i.NOS mABC1 mHMGCoAS V1.y C14.0 Min. :-1.0200 Min. :-1.230 Min. :-1.250 Min. :-0.8900 Min. :-1.890 Min. :-1.300 Min. :-1.430 Min. :-0.9800 Min. :-0.5800 ppar:20 Min. :0.2200 1st Qu.:-0.8950 1st Qu.:-1.100 1st Qu.:-1.173 1st Qu.:-0.8325 1st Qu.:-1.742 1st Qu.:-1.170 1st Qu.:-1.285 1st Qu.:-0.9200 1st Qu.:-0.3000 wt :20 1st Qu.:0.3500 Median :-0.8700 Median :-1.055 Median :-1.135 Median :-0.8000 Median :-1.690 Median :-1.140 Median :-1.240 Median :-0.8700 Median :-0.2100 Median :0.4200 Mean :-0.8485 Mean :-1.058 Mean :-1.138 Mean :-0.7935 Mean :-1.698 Mean :-1.122 Mean :-1.246 Mean :-0.8765 Mean :-0.2210 Mean :0.7630 3rd Qu.:-0.7875 3rd Qu.:-1.020 3rd Qu.:-1.097 3rd Qu.:-0.7475 3rd Qu.:-1.660 3rd Qu.:-1.075 3rd Qu.:-1.208 3rd Qu.:-0.8375 3rd Qu.:-0.1275 3rd Qu.:0.6325 Max. :-0.6900 Max. :-0.840 Max. :-0.980 Max. :-0.6700 Max. :-1.550 Max. :-0.930 Max. :-1.090 Max. :-0.8000 Max. : 0.0600 Max. :3.2400 C16.0 C18.0 C16.1n.9 C16.1n.7 C18.1n.9 C18.1n.7 C20.1n.9 C20.3n.9 C18.2n.6 C18.3n.6 C20.2n.6 Min. :14.65 Min. : 1.680 Min. :0.2900 Min. : 1.590 Min. :14.69 Min. : 1.530 Min. :0.0000 Min. :0.0000 Min. : 2.31 Min. :0.0000 Min. :0.0000 1st Qu.:20.65 1st Qu.: 4.540 1st Qu.:0.4575 1st Qu.: 2.632 1st Qu.:20.05 1st Qu.: 2.140 1st Qu.:0.2450 1st Qu.:0.0000 1st Qu.: 8.88 1st Qu.:0.0000 1st Qu.:0.0000 Median :23.64 Median : 6.500 Median :0.6450 Median : 3.300 Median :23.02 Median : 3.075 Median :0.2850 Median :0.0000 Median :14.87 Median :0.1800 Median :0.1250 Mean :23.03 Mean : 6.747 Mean :0.6870 Mean : 4.419 Mean :25.27 Mean : 4.426 Mean :0.2840 Mean :0.3068 Mean :15.28 Mean :0.3745 Mean :0.1852 3rd Qu.:25.54 3rd Qu.: 9.065 3rd Qu.:0.8125 3rd Qu.: 4.952 3rd Qu.:32.41 3rd Qu.: 4.622 3rd Qu.:0.3725 3rd Qu.:0.2125 3rd Qu.:21.20 3rd Qu.:0.3025 3rd Qu.:0.3025 Max. :29.72 Max. :10.970 Max. :1.5000 Max. :13.900 Max. :41.23 Max. :15.030 Max. :0.6500 Max. :2.8900 Max. :40.02 Max. :5.0700 Max. :0.8300 C20.3n.6 C20.4n.6 C22.4n.6 C22.5n.6 C18.3n.3 C20.3n.3 C20.5n.3 C22.5n.3 C22.6n.3 log.C16.1n.7 Min. :0.110 Min. : 0.750 Min. :0.000 Min. :0.0000 Min. : 0.000 Min. :0.000 Min. :0.00 Min. :0.0000 Min. : 0.280 Min. :0.9517 1st Qu.:0.400 1st Qu.: 1.893 1st Qu.:0.000 1st Qu.:0.0000 1st Qu.: 0.000 1st Qu.:0.000 1st Qu.:0.07 1st Qu.:0.1275 1st Qu.: 1.853 1st Qu.:1.2899 Median :0.725 Median : 3.710 Median :0.025 Median :0.1700 Median : 0.460 Median :0.000 Median :0.25 Median :0.4400 Median : 3.355 Median :1.4586 Mean :0.776 Mean : 5.279 Mean :0.184 Mean :0.4370 Mean : 2.888 Mean :0.091 Mean :1.79 Mean :0.8718 Mean : 5.914 Mean :1.5832 3rd Qu.:1.055 3rd Qu.: 6.270 3rd Qu.:0.310 3rd Qu.:0.4425 3rd Qu.: 1.310 3rd Qu.:0.070 3rd Qu.:2.84 3rd Qu.:1.6750 3rd Qu.:10.393 3rd Qu.:1.7836 Max. :1.640 Max. :15.760 Max. :0.730 Max. :2.5200 Max. :21.620 Max. :0.640 Max. :9.48 Max. :2.5800 Max. :17.350 Max. :2.7014 > library(lattice, pos=18) > library(survival, pos=18) > library(Formula, pos=18) > library(ggplot2, pos=18) > library(Hmisc, pos=18) > rcorr.adjust(total[,c("C14.0","C16.0","C16.1n.7","C16.1n.9","C18.0","C18.1n.7","C18.1n.9","C18.2n.6","C18.3n.3","C18.3n.6","C20.1n.9","C20.2n.6","C20.3n.3", "C20.3n.6","C20.3n.9","C20.4n.6","C20.5n.3","C22.4n.6","C22.5n.3","C22.5n.6","C22.6n.3")], type="pearson", use="complete") Pearson correlations: C14.0 C16.0 C16.1n.7 C16.1n.9 C18.0 C18.1n.7 C18.1n.9 C18.2n.6 C18.3n.3 C18.3n.6 C20.1n.9 C20.2n.6 C20.3n.3 C20.3n.6 C20.3n.9 C20.4n.6 C20.5n.3 C22.4n.6 C22.5n.3 C22.5n.6 C14.0 1.0000 0.0093 0.9720 0.6574 -0.5909 0.8938 0.6949 -0.5071 -0.1578 0.1533 0.1248 -0.3210 -0.1906 -0.4490 0.3261 -0.3106 -0.3318 -0.2817 -0.2727 -0.1428 C16.0 0.0093 1.0000 0.0184 -0.3721 0.5559 0.1138 -0.2042 -0.6629 -0.3684 -0.0522 -0.5048 -0.5618 -0.1474 0.3973 0.3026 0.1757 0.2626 -0.3040 0.1827 -0.0609 C16.1n.7 0.9720 0.0184 1.0000 0.6477 -0.6120 0.8930 0.7071 -0.5698 -0.0477 0.1395 0.0443 -0.3963 -0.0746 -0.4682 0.3464 -0.3482 -0.2764 -0.3312 -0.2719 -0.2106 C16.1n.9 0.6574 -0.3721 0.6477 1.0000 -0.8964 0.7148 0.9141 -0.0385 -0.1546 0.0279 0.1883 0.0449 -0.2496 -0.5838 0.1069 -0.3855 -0.5248 -0.1243 -0.4528 -0.1647 C18.0 -0.5909 0.5559 -0.6120 -0.8964 1.0000 -0.5728 -0.8399 -0.0843 -0.0785 -0.1138 -0.2780 -0.0825 0.0727 0.7119 -0.1119 0.5513 0.4442 0.1745 0.2902 0.2692 C18.1n.7 0.8938 0.1138 0.8930 0.7148 -0.5728 1.0000 0.8003 -0.5564 -0.3111 0.2747 -0.0082 -0.2941 -0.3168 -0.2966 0.5200 -0.1693 -0.4625 -0.1841 -0.3801 -0.0316 C18.1n.9 0.6949 -0.2042 0.7071 0.9141 -0.8399 0.8003 1.0000 -0.2342 -0.2247 0.2188 0.1114 -0.1347 -0.3005 -0.4906 0.3798 -0.3594 -0.5589 -0.2260 -0.4124 -0.2264 C18.2n.6 -0.5071 -0.6629 -0.5698 -0.0385 -0.0843 -0.5564 -0.2342 1.0000 -0.0579 -0.1547 0.2630 0.8612 -0.1635 0.0811 -0.5004 0.1548 -0.1928 0.5913 -0.2186 0.2774 C18.3n.3 -0.1578 -0.3684 -0.0477 -0.1546 -0.0785 -0.3111 -0.2247 -0.0579 1.0000 -0.1600 0.2266 -0.2114 0.9108 -0.4435 -0.2116 -0.3707 0.4835 -0.2806 0.4036 -0.3201 C18.3n.6 0.1533 -0.0522 0.1395 0.0279 -0.1138 0.2747 0.2188 -0.1547 -0.1600 1.0000 0.2942 -0.0101 -0.1768 0.0329 0.6756 0.0546 -0.2752 0.0316 0.2546 0.1427 C20.1n.9 0.1248 -0.5048 0.0443 0.1883 -0.2780 -0.0082 0.1114 0.2630 0.2266 0.2942 1.0000 0.3478 0.2309 -0.3311 -0.0111 -0.1262 -0.0529 0.1670 0.1790 0.0913 C20.2n.6 -0.3210 -0.5618 -0.3963 0.0449 -0.0825 -0.2941 -0.1347 0.8612 -0.2114 -0.0101 0.3478 1.0000 -0.2784 0.2467 -0.2988 0.4157 -0.4139 0.8247 -0.4330 0.5897 C20.3n.3 -0.1906 -0.1474 -0.0746 -0.2496 0.0727 -0.3168 -0.3005 -0.1635 0.9108 -0.1768 0.2309 -0.2784 1.0000 -0.3786 -0.2185 -0.3777 0.7090 -0.3028 0.4866 -0.3393 C20.3n.6 -0.4490 0.3973 -0.4682 -0.5838 0.7119 -0.2966 -0.4906 0.0811 -0.4435 0.0329 -0.3311 0.2467 -0.3786 1.0000 0.0098 0.8883 -0.1789 0.5992 -0.2451 0.6319 C20.3n.9 0.3261 0.3026 0.3464 0.1069 -0.1119 0.5200 0.3798 -0.5004 -0.2116 0.6756 -0.0111 -0.2988 -0.2185 0.0098 1.0000 -0.0055 -0.2955 -0.2086 0.1065 -0.0017 C20.4n.6 -0.3106 0.1757 -0.3482 -0.3855 0.5513 -0.1693 -0.3594 0.1548 -0.3707 0.0546 -0.1262 0.4157 -0.3777 0.8883 -0.0055 1.0000 -0.3909 0.7820 -0.4391 0.8296 C20.5n.3 -0.3318 0.2626 -0.2764 -0.5248 0.4442 -0.4625 -0.5589 -0.1928 0.4835 -0.2752 -0.0529 -0.4139 0.7090 -0.1789 -0.2955 -0.3909 1.0000 -0.4644 0.6975 -0.4367 C22.4n.6 -0.2817 -0.3040 -0.3312 -0.1243 0.1745 -0.1841 -0.2260 0.5913 -0.2806 0.0316 0.1670 0.8247 -0.3028 0.5992 -0.2086 0.7820 -0.4644 1.0000 -0.5827 0.8674 C22.5n.3 -0.2727 0.1827 -0.2719 -0.4528 0.2902 -0.3801 -0.4124 -0.2186 0.4036 0.2546 0.1790 -0.4330 0.4866 -0.2451 0.1065 -0.4391 0.6975 -0.5827 1.0000 -0.4372 C22.5n.6 -0.1428 -0.0609 -0.2106 -0.1647 0.2692 -0.0316 -0.2264 0.2774 -0.3201 0.1427 0.0913 0.5897 -0.3393 0.6319 -0.0017 0.8296 -0.4367 0.8674 -0.4372 1.0000 C22.6n.3 -0.4793 0.4546 -0.5020 -0.5906 0.5695 -0.5737 -0.6045 -0.0333 -0.0188 -0.2892 -0.3876 -0.3342 0.0462 0.1515 -0.2817 -0.1772 0.5866 -0.4305 0.5881 -0.3877 C22.6n.3 C14.0 -0.4793 C16.0 0.4546 C16.1n.7 -0.5020 C16.1n.9 -0.5906 C18.0 0.5695 C18.1n.7 -0.5737 C18.1n.9 -0.6045 C18.2n.6 -0.0333 C18.3n.3 -0.0188 C18.3n.6 -0.2892 C20.1n.9 -0.3876 C20.2n.6 -0.3342 C20.3n.3 0.0462 C20.3n.6 0.1515 C20.3n.9 -0.2817 C20.4n.6 -0.1772 C20.5n.3 0.5866 C22.4n.6 -0.4305 C22.5n.3 0.5881 C22.5n.6 -0.3877 C22.6n.3 1.0000 Number of observations: 40 Pairwise two-sided p-values: C14.0 C16.0 C16.1n.7 C16.1n.9 C18.0 C18.1n.7 C18.1n.9 C18.2n.6 C18.3n.3 C18.3n.6 C20.1n.9 C20.2n.6 C20.3n.3 C20.3n.6 C20.3n.9 C20.4n.6 C20.5n.3 C22.4n.6 C22.5n.3 C22.5n.6 C14.0 0.9543 <.0001 <.0001 <.0001 <.0001 <.0001 0.0008 0.3309 0.3450 0.4429 0.0434 0.2389 0.0037 0.0400 0.0511 0.0365 0.0783 0.0886 0.3795 C16.0 0.9543 0.9102 0.0180 0.0002 0.4845 0.2063 <.0001 0.0193 0.7489 0.0009 0.0002 0.3639 0.0111 0.0577 0.2782 0.1016 0.0565 0.2593 0.7090 C16.1n.7 <.0001 0.9102 <.0001 <.0001 <.0001 <.0001 0.0001 0.7701 0.3907 0.7859 0.0114 0.6473 0.0023 0.0285 0.0277 0.0842 0.0368 0.0896 0.1920 C16.1n.9 <.0001 0.0180 <.0001 <.0001 <.0001 <.0001 0.8136 0.3408 0.8645 0.2446 0.7833 0.1204 <.0001 0.5114 0.0140 0.0005 0.4446 0.0033 0.3097 C18.0 <.0001 0.0002 <.0001 <.0001 0.0001 <.0001 0.6052 0.6302 0.4844 0.0824 0.6129 0.6558 <.0001 0.4917 0.0002 0.0041 0.2815 0.0693 0.0931 C18.1n.7 <.0001 0.4845 <.0001 <.0001 0.0001 <.0001 0.0002 0.0507 0.0863 0.9597 0.0654 0.0464 0.0631 0.0006 0.2963 0.0027 0.2553 0.0156 0.8467 C18.1n.9 <.0001 0.2063 <.0001 <.0001 <.0001 <.0001 0.1457 0.1634 0.1750 0.4938 0.4073 0.0595 0.0013 0.0157 0.0227 0.0002 0.1609 0.0082 0.1601 C18.2n.6 0.0008 <.0001 0.0001 0.8136 0.6052 0.0002 0.1457 0.7227 0.3405 0.1011 <.0001 0.3135 0.6187 0.0010 0.3402 0.2332 <.0001 0.1754 0.0831 C18.3n.3 0.3309 0.0193 0.7701 0.3408 0.6302 0.0507 0.1634 0.7227 0.3241 0.1597 0.1903 <.0001 0.0041 0.1900 0.0185 0.0016 0.0795 0.0098 0.0441 C18.3n.6 0.3450 0.7489 0.3907 0.8645 0.4844 0.0863 0.1750 0.3405 0.3241 0.0653 0.9507 0.2751 0.8403 <.0001 0.7379 0.0857 0.8466 0.1129 0.3797 C20.1n.9 0.4429 0.0009 0.7859 0.2446 0.0824 0.9597 0.4938 0.1011 0.1597 0.0653 0.0279 0.1518 0.0369 0.9459 0.4378 0.7456 0.3031 0.2691 0.5752 C20.2n.6 0.0434 0.0002 0.0114 0.7833 0.6129 0.0654 0.4073 <.0001 0.1903 0.9507 0.0279 0.0820 0.1249 0.0610 0.0076 0.0079 <.0001 0.0053 <.0001 C20.3n.3 0.2389 0.3639 0.6473 0.1204 0.6558 0.0464 0.0595 0.3135 <.0001 0.2751 0.1518 0.0820 0.0160 0.1756 0.0163 <.0001 0.0575 0.0015 0.0322 C20.3n.6 0.0037 0.0111 0.0023 <.0001 <.0001 0.0631 0.0013 0.6187 0.0041 0.8403 0.0369 0.1249 0.0160 0.9519 <.0001 0.2693 <.0001 0.1274 <.0001 C20.3n.9 0.0400 0.0577 0.0285 0.5114 0.4917 0.0006 0.0157 0.0010 0.1900 <.0001 0.9459 0.0610 0.1756 0.9519 0.9733 0.0641 0.1964 0.5130 0.9918 C20.4n.6 0.0511 0.2782 0.0277 0.0140 0.0002 0.2963 0.0227 0.3402 0.0185 0.7379 0.4378 0.0076 0.0163 <.0001 0.9733 0.0126 <.0001 0.0046 <.0001 C20.5n.3 0.0365 0.1016 0.0842 0.0005 0.0041 0.0027 0.0002 0.2332 0.0016 0.0857 0.7456 0.0079 <.0001 0.2693 0.0641 0.0126 0.0025 <.0001 0.0048 C22.4n.6 0.0783 0.0565 0.0368 0.4446 0.2815 0.2553 0.1609 <.0001 0.0795 0.8466 0.3031 <.0001 0.0575 <.0001 0.1964 <.0001 0.0025 <.0001 <.0001 C22.5n.3 0.0886 0.2593 0.0896 0.0033 0.0693 0.0156 0.0082 0.1754 0.0098 0.1129 0.2691 0.0053 0.0015 0.1274 0.5130 0.0046 <.0001 <.0001 0.0048 C22.5n.6 0.3795 0.7090 0.1920 0.3097 0.0931 0.8467 0.1601 0.0831 0.0441 0.3797 0.5752 <.0001 0.0322 <.0001 0.9918 <.0001 0.0048 <.0001 0.0048 C22.6n.3 0.0018 0.0032 0.0010 <.0001 0.0001 0.0001 <.0001 0.8385 0.9082 0.0703 0.0135 0.0351 0.7769 0.3508 0.0782 0.2740 <.0001 0.0056 <.0001 0.0135 C22.6n.3 C14.0 0.0018 C16.0 0.0032 C16.1n.7 0.0010 C16.1n.9 <.0001 C18.0 0.0001 C18.1n.7 0.0001 C18.1n.9 <.0001 C18.2n.6 0.8385 C18.3n.3 0.9082 C18.3n.6 0.0703 C20.1n.9 0.0135 C20.2n.6 0.0351 C20.3n.3 0.7769 C20.3n.6 0.3508 C20.3n.9 0.0782 C20.4n.6 0.2740 C20.5n.3 <.0001 C22.4n.6 0.0056 C22.5n.3 <.0001 C22.5n.6 0.0135 C22.6n.3 Adjusted p-values (Holm's method) C14.0 C16.0 C16.1n.7 C16.1n.9 C18.0 C18.1n.7 C18.1n.9 C18.2n.6 C18.3n.3 C18.3n.6 C20.1n.9 C20.2n.6 C20.3n.3 C20.3n.6 C20.3n.9 C20.4n.6 C20.5n.3 C22.4n.6 C22.5n.3 C22.5n.6 C14.0 1.0000 <.0001 0.0008 0.0108 <.0001 0.0001 0.1370 1.0000 1.0000 1.0000 1.0000 1.0000 0.5488 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 C16.0 1.0000 1.0000 1.0000 0.0327 1.0000 1.0000 0.0006 1.0000 1.0000 0.1448 0.0275 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 C16.1n.7 <.0001 1.0000 0.0012 0.0050 <.0001 <.0001 0.0214 1.0000 1.0000 1.0000 1.0000 1.0000 0.3588 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 C16.1n.9 0.0008 1.0000 0.0012 <.0001 <.0001 <.0001 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.0135 1.0000 1.0000 0.0839 1.0000 0.5053 1.0000 C18.0 0.0108 0.0327 0.0050 <.0001 0.0194 <.0001 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 <.0001 1.0000 0.0377 0.6089 1.0000 1.0000 1.0000 C18.1n.7 <.0001 1.0000 <.0001 <.0001 0.0194 <.0001 0.0324 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.0957 1.0000 0.4067 1.0000 1.0000 1.0000 C18.1n.9 0.0001 1.0000 <.0001 <.0001 <.0001 <.0001 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.2084 1.0000 1.0000 0.0301 1.0000 1.0000 1.0000 C18.2n.6 0.1370 0.0006 0.0214 1.0000 1.0000 0.0324 1.0000 1.0000 1.0000 1.0000 <.0001 1.0000 1.0000 0.1615 1.0000 1.0000 0.0107 1.0000 1.0000 C18.3n.3 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 <.0001 0.6141 1.0000 1.0000 0.2470 1.0000 1.0000 1.0000 C18.3n.6 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.0003 1.0000 1.0000 1.0000 1.0000 1.0000 C20.1n.9 1.0000 0.1448 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 C20.2n.6 1.0000 0.0275 1.0000 1.0000 1.0000 1.0000 1.0000 <.0001 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 <.0001 0.7567 0.0112 C20.3n.3 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 <.0001 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 <.0001 1.0000 0.2299 1.0000 C20.3n.6 0.5488 1.0000 0.3588 0.0135 <.0001 1.0000 0.2084 1.0000 0.6141 1.0000 1.0000 1.0000 1.0000 1.0000 <.0001 1.0000 0.0081 1.0000 0.0023 C20.3n.9 1.0000 1.0000 1.0000 1.0000 1.0000 0.0957 1.0000 0.1615 1.0000 0.0003 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 C20.4n.6 1.0000 1.0000 1.0000 1.0000 0.0377 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 <.0001 1.0000 1.0000 <.0001 0.6749 <.0001 C20.5n.3 1.0000 1.0000 1.0000 0.0839 0.6089 0.4067 0.0301 1.0000 0.2470 1.0000 1.0000 1.0000 <.0001 1.0000 1.0000 1.0000 0.3910 0.0001 0.7022 C22.4n.6 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.0107 1.0000 1.0000 1.0000 <.0001 1.0000 0.0081 1.0000 <.0001 0.3910 0.0139 <.0001 C22.5n.3 1.0000 1.0000 1.0000 0.5053 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.7567 0.2299 1.0000 1.0000 0.6749 0.0001 0.0139 0.6994 C22.5n.6 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.0112 1.0000 0.0023 1.0000 <.0001 0.7022 <.0001 0.6994 C22.6n.3 0.2732 0.4880 0.1555 0.0109 0.0215 0.0190 0.0067 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 0.0123 0.7950 0.0117 1.0000 C22.6n.3 C14.0 0.2732 C16.0 0.4880 C16.1n.7 0.1555 C16.1n.9 0.0109 C18.0 0.0215 C18.1n.7 0.0190 C18.1n.9 0.0067 C18.2n.6 1.0000 C18.3n.3 1.0000 C18.3n.6 1.0000 C20.1n.9 1.0000 C20.2n.6 1.0000 C20.3n.3 1.0000 C20.3n.6 1.0000 C20.3n.9 1.0000 C20.4n.6 1.0000 C20.5n.3 0.0123 C22.4n.6 0.7950 C22.5n.3 0.0117 C22.5n.6 1.0000 C22.6n.3 > load("biostat1-data.RData") > ls() [1] "diet" "gene" "genotype" "lipid" "lipid.Z" "total" > scatterplot(C16.0~C14.0, reg.line=lm, smooth=TRUE, spread=FALSE, id.method='identify', boxplots='xy', span=0.5, ellipse=TRUE, levels=c(.5, .9), pch=c("+"), data=total) [1] "10" "21" "31" "32" "36" "6" > scatterplot(C16.1n.7~C14.0, log="xy", reg.line=lm, smooth=TRUE, spread=FALSE, id.method='mahal', id.n = 2, boxplots='xy', span=0.5, ellipse=FALSE, levels=c(.5, .9), pch=c("+"), data=total) 31 38 25 32 > scatterplotMatrix(~C14.0+C16.0+C16.1n.7+C16.1n.9, reg.line=lm, smooth=FALSE, spread=FALSE, span=0.5, ellipse=FALSE, levels=c(.5, .9), id.n=0, diagonal = 'density', data=total) > scatterplotMatrix(~log(C14.0+1)+log(C16.0+1)+log(C16.1n.7+1)+log(C16.1n.9+1), reg.line=lm, smooth=FALSE, spread=FALSE, span=0.5, ellipse=FALSE, levels=c(.5, .9), id.n=0, diagonal = 'density', data=total) > library(abind, pos=15) > library(e1071, pos=16) > numSummary(total[,"C14.0"], groups=total$diet, statistics=c("mean", "sd"), quantiles=c(0,.25,.5,.75,1)) mean sd data:n coc 2.15000 0.86818365 8 fish 0.32375 0.08551316 8 lin 0.45500 0.15757085 8 ref 0.48625 0.11891624 8 sun 0.40000 0.07151423 8 > Boxplot(C14.0~diet, data=total, id.method="y") > with(total, Hist(C14.0, groups=diet, scale="frequency", breaks="Sturges", col="darkgray")) > stripchart(C14.0 ~ diet, vertical=TRUE, method="stack", ylab="C14.0", data=total) > local({ + .Table <- xtabs(~diet+genotype, data=total) + cat("\nFrequency table:\n") + print(.Table) + cat("\nColumn percentages:\n") + print(colPercents(.Table)) + }) Frequency table: genotype diet ppar wt coc 4 4 fish 4 4 lin 4 4 ref 4 4 sun 4 4 Column percentages: genotype diet ppar wt coc 20 20 fish 20 20 lin 20 20 ref 20 20 sun 20 20 Total 100 100 Count 20 20 > with(total, Barplot(genotype, by=diet, style="divided", legend.pos="topright", xlab="genotype", ylab="Frequency")) > numSummary(gene[,c("ACAT1", "ACAT2")], statistics=c("mean"), quantiles=c(0,.25,.5,.75,1)) mean n ACAT1 -0.65525 40 ACAT2 -0.76675 40 > with(gene, median(ACAT1 - ACAT2, na.rm=TRUE)) # median difference [1] 0.145 > with(gene, wilcox.test(ACAT1, ACAT2, alternative='two.sided', paired=TRUE)) Wilcoxon signed rank test with continuity correction data: ACAT1 and ACAT2 V = 623, p-value = 0.001174 alternative hypothesis: true location shift is not equal to 0 > with(gene, (t.test(ACAT1, ACAT2, alternative='two.sided', conf.level=.95, paired=TRUE))) Paired t-test data: ACAT1 and ACAT2 t = 3.769, df = 39, p-value = 0.0005427 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: 0.0516612 0.1713388 sample estimates: mean of the differences 0.1115 > numSummary(lipid[,"C14.0"], statistics=c("mean"), quantiles=c(0,.25,.5,.75,1)) mean 0.763 > with(lipid, median(C14.0, na.rm=TRUE)) [1] 0.42 > with(lipid, mean(C14.0, na.rm=TRUE)) [1] 0.763 > with(lipid, wilcox.test(C14.0, alternative='two.sided', mu=1)) Wilcoxon signed rank test with continuity correction data: C14.0 V = 194.5, p-value = 0.003848 alternative hypothesis: true location is not equal to 1 > with(lipid, (t.test(C14.0, alternative='two.sided', mu=1, conf.level=.95))) One Sample t-test data: C14.0 t = -1.8723, df = 39, p-value = 0.06867 alternative hypothesis: true mean is not equal to 1 95 percent confidence interval: 0.506966 1.019034 sample estimates: mean of x 0.763 > library(nortest, pos=17) > with(lipid, shapiro.test(C14.0)) Shapiro-Wilk normality test data: C14.0 W = 0.62374, p-value = 6.697e-09 > Boxplot( ~ C14.0, data=lipid, id.method="y") [1] "6" "10" "17" "19" "21" "31" "32" "36" > with(total, tapply(C14.0, genotype, median, na.rm=TRUE)) ppar wt 0.57 0.35 > wilcox.test(C14.0 ~ genotype, alternative="two.sided", data=total) Wilcoxon rank sum test with continuity correction data: C14.0 by genotype W = 326, p-value = 0.0006808 alternative hypothesis: true location shift is not equal to 0 > t.test(C14.0~genotype, alternative='two.sided', conf.level=.95, var.equal=FALSE, data=total) Welch Two Sample t-test data: C14.0 by genotype t = 1.8126, df = 26.386, p-value = 0.08129 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: -0.05941223 0.95141223 sample estimates: mean in group ppar mean in group wt 0.986 0.540 > with(total, shapiro.test(C14.0)) Shapiro-Wilk normality test data: C14.0 W = 0.62374, p-value = 6.697e-09 > with(total, tapply(C14.0, genotype, var, na.rm=TRUE)) ppar wt 1.0070884 0.2037684 > var.test(C14.0 ~ genotype, alternative='two.sided', conf.level=.95, data=total) F test to compare two variances data: C14.0 by genotype F = 4.9423, num df = 19, denom df = 19, p-value = 0.001043 alternative hypothesis: true ratio of variances is not equal to 1 95 percent confidence interval: 1.95623 12.48652 sample estimates: ratio of variances 4.942318 > total$C14.0.bin <- with(total, bin.var(C14.0, bins=2, method='proportions', labels=NULL)) > local({ + .Table <- with(total, table(C14.0.bin)) + cat("\ncounts:\n") + print(.Table) + cat("\npercentages:\n") + print(round(100*.Table/sum(.Table), 2)) + }) counts: C14.0.bin [0.22,0.42] (0.42,3.24] 20 20 percentages: C14.0.bin [0.22,0.42] (0.42,3.24] 50 50 > local({ + .Table <- xtabs(~diet+C14.0.bin, data=total) + cat("\nFrequency table:\n") + print(.Table) + cat("\nColumn percentages:\n") + print(colPercents(.Table)) + }) Frequency table: C14.0.bin diet [0.22,0.42] (0.42,3.24] coc 0 8 fish 7 1 lin 4 4 ref 3 5 sun 6 2 Column percentages: C14.0.bin diet [0.22,0.42] (0.42,3.24] coc 0 40 fish 35 5 lin 20 20 ref 15 25 sun 30 10 Total 100 100 Count 20 20 > local({ + .Table <- xtabs(~diet+C14.0.bin, data=total) + cat("\nFrequency table:\n") + print(.Table) + print(fisher.test(.Table)) + }) Frequency table: C14.0.bin diet [0.22,0.42] (0.42,3.24] coc 0 8 fish 7 1 lin 4 4 ref 3 5 sun 6 2 Fisher's Exact Test for Count Data data: .Table p-value = 0.003737 alternative hypothesis: two.sided > local({ + .Table <- xtabs(~diet+C14.0.bin, data=total) + cat("\nFrequency table:\n") + print(.Table) + .Test <- chisq.test(.Table, correct=FALSE) + print(.Test) + cat("\nExpected counts:\n") + print(.Test$expected) + }) Frequency table: C14.0.bin diet [0.22,0.42] (0.42,3.24] coc 0 8 fish 7 1 lin 4 4 ref 3 5 sun 6 2 Pearson's Chi-squared test data: .Table X-squared = 15, df = 4, p-value = 0.004701 Expected counts: C14.0.bin diet [0.22,0.42] (0.42,3.24] coc 4 4 fish 4 4 lin 4 4 ref 4 4 sun 4 4