filterRes {InPAS} | R Documentation

## 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

### 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)

[Package InPAS version 1.16.3 Index]