EnrichAB: Enrichment analysis for Positive and Negative selection genes

In WubingZhang/MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

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 Positive and Negative

Usage

EnrichAB(
  data,
  enrich_method = "HGT",
  top = 10,
  limit = c(2, 100),
  filename = NULL,
  out.dir = ".",
  width = 6.5,
  height = 4,
  verbose = TRUE,
  ...
)

Arguments

data	A data frame.
enrich_method	One of "ORT" (Over-Representing Test) and "HGT" (HyperGemetric test).
top	An integer, specifying the number of pathways to show.
limit	A two-length vector, 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.
verbose	Boolean
...	Other available parameters in ggsave.

Value

A list containing enrichment results for each group genes. This list contains eight items, which contain subitems of gridPlot and enrichRes.

Author(s)

Wubing Zhang

WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.