filterRes {InPAS} | R Documentation |
filter results of testUsage
filterRes(res, gp1, gp2, background_coverage_threshold=2, P.Value_cutoff=0.05, adj.P.Val_cutoff=0.05, dPDUI_cutoff=0.3, PDUI_logFC_cutoff)
res |
output of testUsage |
gp1 |
tag names involved in group 1 |
gp2 |
tag names involved in group 2 |
background_coverage_threshold |
background coverage cut off value. for each group, more than half of the long form should greater than background_coverage_threshold. for both group, at leat in one group, more than half of the short form should greater than background_coverage_threshold. |
P.Value_cutoff |
cutoff of P value |
adj.P.Val_cutoff |
cutoff of adjust P value |
dPDUI_cutoff |
cutoff of dPDUI |
PDUI_logFC_cutoff |
cutoff of PDUI log2 transformed fold change |
a data.frame
Jianhong Ou
path <- file.path(find.package("InPAS"), "extdata") load(file.path(path, "CPs.MAQC.rda")) load(file.path(path, "coverage.MAQC.rda")) library(BSgenome.Hsapiens.UCSC.hg19) data(utr3.hg19) res <- testUsage(CPsites=CPs, coverage=coverage, genome=BSgenome.Hsapiens.UCSC.hg19, utr3=utr3.hg19, method="fisher.exact", gp1=c("Brain.auto", "Brain.phiX"), gp2=c("UHR.auto", "UHR.phiX")) filterRes(res, gp1=c("Brain.auto", "Brain.phiX"), gp2=c("UHR.auto", "UHR.phiX"), background_coverage_threshold=2, P.Value_cutoff=0.05, adj.P.Val_cutoff=0.05, dPDUI_cutoff=0.3, PDUI_logFC_cutoff=.59)