diff GO_deltaRanks_correlation.R @ 0:91261b42c07e draft

"planemo upload commit 25eebba0c98dd7a5a703412be90e97f13f66b5bc"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GO_deltaRanks_correlation.R	Thu Apr 14 13:28:05 2022 +0000
@@ -0,0 +1,32 @@
+#setwd("~/Dropbox/Documents/dixon_2017_RT-GBM/reciprocal_transplant_methylationV2/clean_july12/scripts")
+
+data1=read.table("MWU_MF_heat_lpv.csv",header=T)
+data2=read.table("MWU_MF_surv_lpv.csv",header=T)
+
+goods=intersect(data1$term,data2$term)
+#goods=unique(as.character(c(data1$term[data1$p.adj<=0.1],data2$term[data2$p.adj<=0.1])))
+length(goods)
+
+data1=data1[data1$term %in% goods,]
+data2=data2[data2$term %in% goods,]
+
+# all overlapping GO terms
+ress=merge(data1,data2,by="term")
+plot(delta.rank.x~delta.rank.y,ress,xlab="GBM", ylab="GE",mgp=c(2.3,1,0))
+abline(v=0,lty=3)
+abline(h=0,lty=3)
+
+# GO terms highly signifcant in any of the two datasets
+sigs=(ress$p.adj.x<=0.01 | ress$p.adj.y<=0.01)
+sum(sigs) # 71
+plot(delta.rank.x~delta.rank.y,ress[sigs,],xlab="GBM", ylab="GE",mgp=c(2.3,1,0))
+abline(v=0,lty=3)
+abline(h=0,lty=3)
+
+# GO terms signifcant in both datasets
+sigs=(ress$p.adj.x<=0.1 & ress$p.adj.y<=0.1)
+sum(sigs) # 20
+plot(delta.rank.x~delta.rank.y,ress[sigs,],xlab="GBM", ylab="GE",mgp=c(2.3,1,0))
+abline(v=0,lty=3)
+abline(h=0,lty=3)
+