filterRes: filter results

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

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

Author(s)

Jianhong Ou

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)

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.