annotate GO_deltaRanks_correlation.R @ 2:5acf9dfdfa27 draft default tip

planemo upload commit 66a856bcce69986d9a6f1a39820dd9b3f4f6b0db
author cristian
date Wed, 09 Nov 2022 08:57:54 +0000
parents 91261b42c07e
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1 #setwd("~/Dropbox/Documents/dixon_2017_RT-GBM/reciprocal_transplant_methylationV2/clean_july12/scripts")
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3 data1=read.table("MWU_MF_heat_lpv.csv",header=T)
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4 data2=read.table("MWU_MF_surv_lpv.csv",header=T)
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6 goods=intersect(data1$term,data2$term)
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7 #goods=unique(as.character(c(data1$term[data1$p.adj<=0.1],data2$term[data2$p.adj<=0.1])))
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8 length(goods)
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10 data1=data1[data1$term %in% goods,]
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11 data2=data2[data2$term %in% goods,]
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12
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13 # all overlapping GO terms
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14 ress=merge(data1,data2,by="term")
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15 plot(delta.rank.x~delta.rank.y,ress,xlab="GBM", ylab="GE",mgp=c(2.3,1,0))
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16 abline(v=0,lty=3)
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17 abline(h=0,lty=3)
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19 # GO terms highly signifcant in any of the two datasets
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20 sigs=(ress$p.adj.x<=0.01 | ress$p.adj.y<=0.01)
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21 sum(sigs) # 71
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22 plot(delta.rank.x~delta.rank.y,ress[sigs,],xlab="GBM", ylab="GE",mgp=c(2.3,1,0))
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23 abline(v=0,lty=3)
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24 abline(h=0,lty=3)
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25
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26 # GO terms signifcant in both datasets
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27 sigs=(ress$p.adj.x<=0.1 & ress$p.adj.y<=0.1)
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28 sum(sigs) # 20
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29 plot(delta.rank.x~delta.rank.y,ress[sigs,],xlab="GBM", ylab="GE",mgp=c(2.3,1,0))
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30 abline(v=0,lty=3)
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31 abline(h=0,lty=3)
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32