EnrichSquare: Enrichment analysis for selected treatment related genes

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

Description

Do enrichment analysis for selected treatment related genes in 9-squares

Usage

EnrichSquare(
  beta,
  id = "Gene",
  keytype = "Symbol",
  x = "Control",
  y = "Treatment",
  pvalue = 0.05,
  enrich_method = "ORT",
  organism = "hsa",
  limit = c(1, 120),
  filename = NULL,
  out.dir = ".",
  width = 6.5,
  height = 4,
  verbose = TRUE,
  ...
)

Arguments

beta	Data frame, with columns of "Gene", "group", and "Diff".
id	A character, indicating the gene column in the data.
keytype	A character, "Symbol" or "Entrez".
x	A character, indicating the x-axis in the 9-square scatter plot.
y	A character, indicating the y-axis in the 9-square scatter plot.
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. NULL(default) means no output.
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. Each item in the returned list has two sub items:

gridPlot	an object created by ggplot, which can be assigned and further customized.
enrichRes	a enrichResult instance.

Author(s)

Wubing Zhang

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