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", limit = c(1, 120), filename = NULL,
  out.dir = ".", width = 6.5, height = 4, ...)

Arguments

`data`	A data frame.
`pvalue`	Pvalue cutoff.
`enrich_method`	One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test).
`organism`	"hsa" or "mmu".
`limit`	A two-length vector (default: c(1, 120)), specifying the min and max size of pathways for enrichent analysis.
`filename`	Suffix of output file name.
`out.dir`	Path to save plot to (combined with filename).
`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, goA, goB. 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)

Binbin Wang

Examples

data(mle.gene_summary)
# Read beta score from gene summary table in MAGeCK MLE results
dd = ReadBeta(mle.gene_summary)
data=ScatterView(dd, ctrlname = "dmso", treatname = "plx")$data
## Not run: 
  #GO and KEGG enrichment analysis
 enrich_result = EnrichAB(data, pvalue=0.05, organism="hsa")
  print(enrich_result$keggA$gridPlot)
  print(enrich_result$goA$gridPlot)

## End(Not run)

[Package MAGeCKFlute version 1.4.3 Index]