filter_testOut {InPAS} | R Documentation

## filter 3' UTR usage test results

### Description

filter results of `test_dPDUI()`

### Usage

    filter_testOut(
      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` | a UTR3eSet object, output of `test_dPDUI()`
`gp1` | tag names involved in group 1. gp1 and gp2 are used for filtering purpose if both are specified; otherwise only other specified thresholds are used for filtering.
`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 least 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 converted from an object of GenomicRanges::GRanges.

### Author(s)

Jianhong Ou, Haibo Liu

### See Also

`test_dPDUI()`

### Examples

    library(limma)
    path <- system.file("extdata", package = "InPAS")
    load(file.path(path, "eset.MAQC.rda"))
    tags <- colnames(eset@PDUI)
    g <- factor(gsub("\\..*$", "", tags))
    design <- model.matrix(~ -1 + g)
    colnames(design) <- c("Brain", "UHR")
    contrast.matrix <- makeContrasts(contrasts = "Brain-UHR",
                                     levels = design)
    res <- test_dPDUI(eset = eset,
                      method = "limma",
                      normalize = "none",
                      design = design,
                      contrast.matrix = contrast.matrix)
    filter_testOut(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 2.2.0 Index]