filter_testOut: filter 3' UTR usage test results

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

filter 3' UTR usage test results

Description

filter results of test_dPDUI()

Usage

filter_testOut(
  res,
  gp1,
  gp2,
  outdir = getInPASOutputDirectory(),
  background_coverage_threshold = 2,
  P.Value_cutoff = 0.05,
  adj.P.Val_cutoff = 0.05,
  dPDUI_cutoff = 0.2,
  PDUI_logFC_cutoff = log2(1.5)
)

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
outdir	A character(1) vector, a path with write permission for storing InPAS analysis results. If it doesn't exist, it will be created.
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
)

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.