Mercurial > repos > laurenmarazzi > netisce_test
view tools/myTools/bin/crit2.R @ 1:7e5c71b2e71f draft default tip
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author | laurenmarazzi |
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date | Wed, 22 Dec 2021 16:00:34 +0000 |
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#!/usr/bin/env Rscript .libPaths('~/R_libs_36') args = commandArgs(trailingOnly=TRUE) library(plyr) library("dplyr", warn.conflicts = FALSE) library(reshape2) library(readr) getwd() exp<-read.delim(args[1],sep=" ",row.names = 1) samples<-read.delim(args[2],sep="\t",row.names = 1) exp<-exp %>% dplyr::filter(row.names(exp) %in% row.names(samples)) desired<-args[3] undesired<-args[4] filter<-args[5] dfdes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% desired,,drop=FALSE])) meandes<- apply(dfdes,2,mean) dfundes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% undesired,,drop=FALSE])) meandundes<-apply(dfundes,2,mean) test<-meandes-meandundes disc<-test disc[disc<0]<-0 disc[disc>0]<-1 nodes<-colnames(dfdes) is<-read.delim(args[6],sep=" ") #internal_markers.txt isdisc<-is if (filter=="strict"){ for (node in nodes){ if (disc[node]==0){ val=max(dfdes[,node]) isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0) isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1) } if (disc[node]==1){ val=min(dfdes[,node]) isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1) isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0) } } }else { #filter=="relaxed" for (node in nodes){ if (disc[node]==0){ val=min(dfundes[,node]) isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0) isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1) } if (disc[node]==1){ val=max(dfdes[,node]) isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1) isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0) } } } hammings<-data.frame(isdisc$replicate,isdisc$perturbation) colnames(hammings)=c("replicate","perturbation") hammings$hammingdist<-sapply(isdisc[,3],function(x) sum(disc != x)) if (length(nodes)<10){ hams1_1<-hammings %>%filter(hammingdist<1) }else{ hams1_1<-hammings %>%filter(hammingdist<=length(nodes)-round(.9*length(nodes))) } write.table(hams1_1[,c(1,2)],'crit2_perturbations.txt',quote=FALSE,row.names = FALSE,sep=" ")