callQoRT: Use QoRTs to get the count of subfeatures in each gene

In aiminy/PathwaySJ: A R package for GO term enrichment analysis with the flexible bias factor adjustment

Description

Use QoRTs to get the count of subfeatures in each gene

Usage

callQoRT(input_file, runing_cmd, gtf_file)

Examples

dir.name="/media/H_driver/Aimin_project/GOSJ_example_data/"
dir.name="/media/H_driver/Aimin_project/GOSJ_STAR_Bam/"

file.name=dir(dir.name,recursive = TRUE,pattern="sorted.bam")
file.name.whole<-paste0(dir.name,file.name)
file.name.selected<-file.name.whole
file.name.selected.2<-as.list(file.name.selected)
names(file.name.selected.2)=sapply(strsplit(file.name.selected,split="\\/"),"[[",6)

file.name.selected.3<-file.name.selected.2[-c(1,3)]

cmd1="java -Xmx4000M -jar /home/aiminyan/QoRTs/QoRTsFullExampleData/QoRTsRelease/QoRTs.jar QC --noGzipOutput --keepMultiMapped"

cmd2="java -Xmx5000M -jar /home/aiminyan/QoRTs/QoRTsFullExampleData/QoRTsRelease/QoRTs.jar QC --noGzipOutput"

gtf1="/media/H_driver/Aimin_project/GTF_Files/Homo_sapiens.GRCh38.84.processed.sorted.2.gtf"

re.out<-lapply(file.name.selected.3,callQoRT,gtf_file=gtf1,runing_cmd=cmd2)

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