EnrichAB: Enrichment analysis for Positive and Negative selection genes

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

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,
  verbose = TRUE,
  ...
)

Arguments

data	A data frame.
pvalue	Pvalue cutoff.
enrich_method	One of "ORT"(Over-Representing Test) 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.
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

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.