summarizeResults.DESeq2: Summarize DESeq2 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)

View source: R/summarizeResults.DESeq2.r

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

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

`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)

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

Hugo Varet

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