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]