get_topGenes_combined: Construction of combined topGenes object from a set of...
In BenaroyaResearch/limmaTools: Helper functions for limma analysis and visualization of results

This function takes a set of pairwise limma model contrasts, and combines the results into a single object.

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get_topGenes_combined(topGenes,
                      topGenes.pairwise,
                      p_cut=0.01, fc_cut=log2(1.5))

`topGenes`	a data frame, typically the output of a call to `topTable`. Must contain genes, log2 fold-change, and adjusted p-values.
`topGenes.pairwise`	a list of data frames, each typically containing the output of a call to `topTable` for a single contrast. Each list element should be named with an identifier for the contrast, and must contain genes, log2 fold-change, and adjusted p-values. Can optionally include a "threshold" column, which should be logical indicating genes passing significance thresholds.
`p_cut`	numeric, the cutoff for adjusted p-value. Genes with adjusted p-values greater than or equal to this value are not considered significant.
`fc_cut`	numeric, the absolute value cutoff for log2 fold change. Genes with absolute value log2-FC less than or equal to this value are not considered significant.

A data frame, with adjusted p-values and logical threshold values for all contrasts in topGenes.pairwise

BenaroyaResearch/limmaTools documentation built on Dec. 17, 2021, 10:49 a.m.

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