signif_hist: Plot histograms of significance (p-value & FDR) columns

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

Plot histograms of significance (p-value & FDR) columns

Description

Plot histograms of significance (p-value & FDR) columns.

Usage

signif_hist(
  tab,
  p.suffix = "p",
  fdr.suffix = "FDR",
  sep = ".",
  pi0 = FALSE,
  name = "signif_hist",
  plot = TRUE,
  nrow = 2
)

Arguments

tab	Table of output from ezlimma.
p.suffix	Suffix for p-value columns. P-value column names cannot be duplicated.
fdr.suffix	Suffix for FDR columns. Set to NA if no FDR columns. FDR column names cannot be duplicated.
sep	Separator for column names before p or FDR, passed to extract_prefix. If not found, it is assumed to be NA.
pi0	Logical indicating if proportion of null hypotheses should be calculated per p-value histogram. If TRUE, propTrueNull with method="convest" is used.
name	Name of file to create. Set to NA to plot to screen instead of to file.
plot	Logical; should plot be generated?
nrow	Number of rows of figures to plot per page

Details

Some p-value columns must be identifiable using p.suffix. If !is.na(fdr.suffix), FDR colnames must have same prefix.

Value

Invisibly, a subset of tab with only columns that contain significances.

jdreyf/ezlimmaplot documentation built on Feb. 8, 2025, 2:25 a.m.