InPAS (version 1.4.4)

filterRes: filter results

Description

filter results of testUsage

Usage

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)

Arguments

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

Value

a data.frame

See Also

testUsage

Examples

    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)