| filter_testOut {InPAS} | R Documentation |
filter results of test_dPDUI()
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 )
res |
a UTR3eSet object, output of |
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 |
A data frame converted from an object of GenomicRanges::GRanges.
Jianhong Ou, Haibo Liu
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)