R: Enrichment analysis for Positive and Negative selection genes

EnrichAB {MAGeCKFlute}

R Documentation

Enrichment analysis for Positive and Negative selection genes

Description

Do enrichment analysis for selected genes, in which positive selection and negative selection are termed as GroupA and GroupB

Usage

EnrichAB(data, pvalue = 0.25, enrich_method = "ORT", organism = "hsa",
  adjust = "BH", filename = NULL, out.dir = ".", gsea = FALSE,
  width = 6.5, height = 4, ...)

Arguments

`data`	A data frame containing columns "diff", with rownames of Entrez IDs.
`pvalue`	Pvalue cutoff.
`enrich_method`	One of "ORT"(Over-Representing Test), "DAVID", "GOstats", and "HGT"(HyperGemetric test).
`organism`	A character, specifying organism, such as "hsa" or "Human"(default), and "mmu" or "Mouse"
`adjust`	One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".
`filename`	Suffix of output file name. NULL(default) means no output.
`out.dir`	Path to save plot to (combined with filename).
`gsea`	Boolean, specifying if do GSEA for GroupA and GroupB genes. Default gsea=FALSE.
`width`	As in ggsave.
`height`	As in ggsave.
`...`	Other available parameters in ggsave.

Value

A list containing enrichment results for each group genes. This list contains items four items, keggA, keggB, bpA, bpB. Four items are all list object, containing subitems of gridPlot and enrichRes. gridPlot is a ggplot object, and enrichRes is a enrichResult instance

Author(s)