GetResultsFromJunctionSeq: Get analysis results using JunctionSeq

Description Usage Arguments Examples

Description

Get analysis results using JunctionSeq

Usage

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GetResultsFromJunctionSeq(dir.name, file.sample, file.count, file.gff)

Arguments

file.gff

Examples

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# For Guoyan Project
load("/Volumes/Bioinformatics\$/2015/Nimer_Cheng/1_29_2016.RData")
dir.name="/Volumes/Bioinformatics$/2015/Nimer_Cheng/"
file.sample="decoder.bySample.txt"
file.count="_junction_seq_new_gtf_7/QC.spliceJunctionAndExonCounts.forJunctionSeq.txt"
file.gff="Mus_musculus.GRCm38.83.JunctionSeq.flat.gff"
Re<-GetResultsFromJunctionSeq(dir.name,file.sample,file.count,file.gff)
head(fData(Re))
save(Re,file="Re_Run_test_GOSJ.RData")

# For PJ project
dir.name.PJ="/media/H_driver/PJ/"
file.sample.PJ="decoder.bySample.rtf"
file.count.PJ="/QC.spliceJunctionAndExonCounts.forJunctionSeq.txt"

file.gff=paste0("/media/H_driver/2015/Nimer_Cheng/",file.gff)
Re.PJ<-GetResultsFromJunctionSeq(dir.name.PJ,file.sample.PJ,file.count.PJ,file.gff)

save(Re.PJ,file="/media/H_driver/PJ/PJ_jscs.RData")
buildAllPlots(jscs=jscs,outfile.prefix="./plots_based_on_DE_splice_site_gene1/",
gene.list=gene.based.de.splice.site[1],use.plotting.device="png",plot.gene.level.expression=TRUE,sequencing.type="single-end");

aiminy/PathwaySJ documentation built on May 10, 2019, 7:38 a.m.