Reference: |
Montgomery S.B., Griffith O.L., Schuetz J.M., Brooks-Wilson, A., Jones S.J.M. "A Computational Discrimination Strategy For Regulatory Polymorphisms In The Upstream Non-Coding Regions of Homo Sapiens" (Submitted). |
R analysis commands an data files
The commands and files used to run the Wilcox Rank Sum test and MTP tests on the rSNP and ufSNP data
Commands
all<-read.table("all.2000.R.table", header=T, row.names=1)
group<-read.table("group.2000.R.table", header=T, row.names=1)
dataa<-numeric()
datag<-numeric()
for(i in 3:length(names(all))) {
if(is.numeric(all[,i])) {
dataa[i]<-wilcox.test(all[,i][!is.na(all[,i]) & all$case=="POSITIVE"], all[,i][!is.na(all[,i]) & all$case=="NEUTRAL"])$p.value
}
}
for(i in 3:length(names(group))) {
if(is.numeric(group[,i])) {
datag[i]<-wilcox.test(group[,i][!is.na(group[,i]) & group$case=="POSITIVE"], group[,i][!is.na(group[,i]) & group$case=="NEUTRAL"])$p.value
}
}
tabledata<-data.frame(cbind(dataa, datag), row.names=names(all))
write.table(tabledata, file="wilcox.results.2000.txt", sep="\t");
library(multtest)
all_variable_data<-t(all[c(3,4,5,6,7,8,9,10,11,13,14,15,16,17,18,19,20,21,22,23,24,25,26)])
group_variable_data<-t(group[c(3,4,5,6,7,8,9,10,11,13,14,15,16,17,18,19,20,21,22,23,24,25,26)])
all_class_labels<-all[,2]
group_class_labels<-group[,2]
MTP_all_results=MTP(X=all_variable_data, Y=all_class_labels, na.rm=TRUE, test="t.twosamp.equalvar", alternative="two.sided", robust=TRUE, typeone="fwer", alpha=0.05, B=10000, method="sd.minP", smooth.null=TRUE)
MTP_group_results=MTP(X=group_variable_data, Y=group_class_labels, na.rm=TRUE, test="t.twosamp.equalvar", alternative="two.sided", robust=TRUE, typeone="fwer", alpha=0.05, B=10000, method="sd.minP", smooth.null=TRUE)
write.table(cbind(MTP_group_results@rawp, MTP_group_results@adjp, MTP_all_results@rawp, MTP_all_results@adjp), file="wilcox.results.2000.test.txt", sep="\t");
dataa2<-numeric()
datag2<-numeric()
for(i in 3:length(names(group))) {
if(is.numeric(group[,i])) {
datag2[i]<-wilcox.test(group[,i][!is.na(group[,i]) & group$case=="POSITIVE"], group[,i][!is.na(group[,i]) & group$case=="NEUTRAL"], conf.int=TRUE)$estimate
}
}
for(i in 3:length(names(all))) {
if(is.numeric(all[,i])) {
dataa2[i]<-wilcox.test(all[,i][!is.na(all[,i]) & all$case=="POSITIVE"], all[,i][!is.na(all[,i]) & all$case=="NEUTRAL"], conf.int=TRUE)$estimate
}
}
cbind(dataa2, names(group))
Files
ALL test file
GROUP test file
ALL test file (unnormalized)
GROUP test file (unnormalized)
ALL test file (152bp)
GROUP test file (152bp)
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