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)

Binbin Wang

See Also

EnrichSquare

data(MLE_Data) # Read beta score from gene summary table in MAGeCK MLE results


[Package MAGeCKFlute version 1.0.1 Index]