summarizeResults.edgeR: Summarize edgeR analysis

Description Usage Arguments Value Author(s)

View source: R/summarizeResults.edgeR.r

Description

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

Usage

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

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)

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


sarangian/RNASeqDEA documentation built on Dec. 8, 2019, 5:24 p.m.