Mercurial > repos > cristian > rbgoa
diff GO_deltaRanks_correlation.R @ 0:91261b42c07e draft
"planemo upload commit 25eebba0c98dd7a5a703412be90e97f13f66b5bc"
author | cristian |
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date | Thu, 14 Apr 2022 13:28:05 +0000 |
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--- /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) +