diff tools/myTools/bin/crit2.R @ 1:7e5c71b2e71f draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/myTools/bin/crit2.R	Wed Dec 22 16:00:34 2021 +0000
@@ -0,0 +1,74 @@
+#!/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=" ")
+
+