s— title: “Analyze GTex Data with Brian’s Summary Data” author: “Chris McKennan” date: ‘2016-05-09’ output: html_document —
Last updated: 2016-05-10
Code version: 5238faba5f48c4dd40de36aff9a0e23341fdea3b
I want to look at the trans eQTLs that we identify in both sun-exposed lower leg and non-sun-exposed suprapubic skin. Since these tissues are similar, we should (in theory) see similar trans-eQTLs in both tissues.
The perl script Overlap2Networks.pl looks for overlap in eQTLs between two tissues. It gives the number of trans-eQTLs that are shared across tissues. It also looks for gene-gene correlation networks that are similar across tissues and looks at the eQTL sharing in those networks. The idea here is if we have two identical networks defined apriori, then we should see similar trans-eQTLs in those networks across tissues.
perl Overlap2Networks.pl ../output/cis_summary_data/skinnotsunexposedsuprapubic/thresh_60 ../output/cis_summary_data/skinsunexposedlowerleg/thresh_60
13% overlap, 193 shared gene-gene correlation networks
perl Overlap2Networks.pl ../output/cis_summary_data/muscleskeletal/thresh_80 ../output/cis_summary_data/adiposesubcutaneous/thresh_80
13% overlap, 23 shared gene-gene correlation networks
perl Overlap2Networks.pl ../output/cis_summary_data/braincaudatebasalganglia/thresh_60 ../output/cis_summary_data/braincaudatebasalganglia/thresh_60
There is NO overlap in these two brain tissues, 0 shared gene-gene correlation networks
Source Gibbs Sampler and Bayes Factor functions.
source("../R/SimulateNetworkExpression.R") #Compute Bayes factors
source("../R/directionality_CGM.R") #Gibbs Sampler
library('gtools')
overlap.file <- "skinnotsunexposedsuprapubic_skinsunexposedlowerleg.OverlapeQTL.txt"
X <- data.frame(read.table(overlap.file, sep="\t", dec=".", comment.char="#", header=T))
ind.nonzero <- which(X$trans.eQTLs_T1 != 0 & X$trans.eQTLs_T2 != 0)
X.nonzero <- X[ind.nonzero,]
N.eQTLs <- apply(cbind(X.nonzero$trans.eQTLs_T1, X.nonzero$trans.eQTLs_T2), 1, min)
ind.1 <- which(N.eQTLs == 1)
frac.shared <- X.nonzero$Shared_trans.eQTLs/N.eQTLs
frac.shared.no1 <- frac.shared[-ind.1]
hist(frac.shared, main="Fraction of eQTLs that are Shared in Overlapping Networks", xlab="#Shared/#trans-eQTLs")
hist(frac.shared.no1, main="Fraction of eQTLs that are Shared in Overlapping Networks, no singletons", xlab="#Shared/#trans-eQTLs")
sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gtools_3.5.0 knitr_1.12.3
loaded via a namespace (and not attached):
[1] magrittr_1.5 formatR_1.3 tools_3.2.4 htmltools_0.3.5
[5] Rcpp_0.12.4 stringi_1.0-1 rmarkdown_0.9.5 stringr_1.0.0
[9] digest_0.6.9 evaluate_0.9