utr3UsageEstimation {InPAS} | R Documentation |
estimation of 3'UTR usage for short form and long form
utr3UsageEstimation(CPsites, coverage, genome, utr3, gp1, gp2=NULL, short_coverage_threshold = 10, long_coverage_threshold = 2, adjusted.P_val.cutoff = 0.05, dPDUI_cutoff = 0.3, PDUI_logFC_cutoff=0.59, BPPARAM=NULL)
CPsites |
outputs of CPsites |
coverage |
coverage for each sample, outputs of coverageFromBedGraph |
genome |
an object of BSgenome |
utr3 |
output of utr3Annotation |
gp1 |
tag names involved in group 1 |
gp2 |
tag names involved in group 2 |
short_coverage_threshold |
cutoff threshold for coverage in thre region of short form |
long_coverage_threshold |
cutoff threshold for coverage in thre region of long form |
adjusted.P_val.cutoff |
cutoff value for adjusted p.value |
dPDUI_cutoff |
cutoff value for differenctial PAS(polyadenylation signal) usage index |
PDUI_logFC_cutoff |
cutoff value for log2 fold change of PAS(polyadenylation signal) usage index |
BPPARAM |
An optional |
return an object of GRanges
Jianhong Ou
if(interactive()){ library(BSgenome.Mmusculus.UCSC.mm10) path <- file.path(find.package("InPAS"), "extdata") bedgraphs <- file.path(path, "Baf3.extract.bedgraph") data(utr3.mm10) tags <- "Baf3" genome <- BSgenome.Mmusculus.UCSC.mm10 coverage <- coverageFromBedGraph(bedgraphs, tags, genome, hugeData=FALSE) CP <- CPsites(coverage=coverage, gp1=tags, gp2=NULL, genome=genome, utr3=utr3.mm10, coverage_threshold=5, long_coverage_threshold=5) res <- utr3UsageEstimation(CP, coverage, utr3.mm10, genome, gp1=tags, gp2=NULL) }