summarizeResults.edgeR: Summarize edgeR analysis

In PF2-pasteur-fr/SARTools: Statistical Analysis of RNA-Seq Tools

Summarize edgeR analysis

Description

Summarize edgeR analysis: diagnotic plots, dispersions plot, summary of the independent filtering, export results...

Usage

summarizeResults.edgeR(
  out.edgeR,
  group,
  counts,
  alpha = 0.05,
  col = c("lightblue", "orange", "MediumVioletRed", "SpringGreen"),
  log2FClim = NULL,
  padjlim = NULL,
  ggplot_theme = theme_light()
)

Arguments

out.edgeR	the result of run.edgeR()
group	factor vector of the condition from which each sample belongs
counts	matrix of raw counts
alpha	significance threshold to apply to the adjusted p-values
col	colors for the plots
log2FClim	numeric vector containing both upper and lower y-axis limits for all the MA-plots produced (NULL by default to set them automatically)
padjlim	numeric value between 0 and 1 for the adjusted p-value upper limits for all the volcano plots produced (NULL by default to set them automatically)
ggplot_theme	ggplot2 theme function (theme_light() by default)

Value

A list containing: (i) a list of data.frames from exportResults.edgeR() and (ii) a table summarizing the number of differentially expressed features

Author(s)

Hugo Varet

PF2-pasteur-fr/SARTools documentation built on April 6, 2022, 2:24 a.m.