summarizeResults.DESeq2: Summarize DESeq2 analysis
In PF2-pasteur-fr/SARTools: Statistical Analysis of RNA-Seq Tools

View source: R/summarizeResults.DESeq2.r

summarizeResults.DESeq2

R Documentation

Summarize DESeq2 analysis

Description

Summarize DESeq2 analysis: diagnotic plots, dispersions plot, summary of the independent filtering, export results...

Usage

summarizeResults.DESeq2(
  out.DESeq2,
  group,
  independentFiltering = TRUE,
  cooksCutoff = TRUE,
  alpha = 0.05,
  col = c("lightblue", "orange", "MediumVioletRed", "SpringGreen"),
  log2FClim = NULL,
  padjlim = NULL,
  ggplot_theme = theme_light()
)

Arguments

`out.DESeq2`	the result of `run.DESeq2()`
`group`	factor vector of the condition from which each sample belongs
`independentFiltering`	`TRUE` or `FALSE` to perform the independent filtering or not
`cooksCutoff`	outliers detection threshold (TRUE to let DESeq2 choosing it or FALSE to disable the outliers detection)
`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.DESeq2(), (ii) the table summarizing the independent filtering procedure and (iii) a table summarizing the number of differentially expressed features