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)