summarizeResults.edgeR: Summarize edgeR analysis
In sarangian/RNASeqDEA: Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups

Description Usage Arguments Value Author(s)

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

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

`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)

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

Hugo Varet

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