SARTools (version 1.6.2)

summarizeResults.DESeq2: 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"))

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

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