EnrichSquare {MAGeCKFlute}R Documentation

Enrichment analysis for selected treatment related genes

Description

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

Usage

EnrichSquare(beta, pvalue = 0.05, enrich_method = "ORT", organism = "hsa",
  adjust = "BH", filename = NULL, out.dir = ".", width = 6.5,
  height = 4, ...)

Arguments

beta

Data frame, which contains column of 'group'.

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).

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 several elements:

kegg1

a list record enriched KEGG pathways for Group1 genes in 9-Square

kegg2

a list record enriched KEGG pathways for Group2 genes in 9-Square

kegg3

a list record enriched KEGG pathways for Group3 genes in 9-Square

kegg4

a list record enriched KEGG pathways for Group4 genes in 9-Square

kegg13

a list record enriched KEGG pathways for Group1&Group3 genes in 9-Square

kegg14

a list record enriched KEGG pathways for Group1&Group4 genes in 9-Square

kegg23

a list record enriched KEGG pathways for Group2&Group3 genes in 9-Square

kegg24

a list record enriched KEGG pathways for Group2&Group4 genes in 9-Square

bp1

a list record enriched GO BP terms for Group1 genes in 9-Square

bp2

a list record enriched GO BP terms for Group2 genes in 9-Square

bp3

a list record enriched GO BP terms for Group3 genes in 9-Square

bp4

a list record enriched GO BP terms for Group4 genes in 9-Square

bp13

a list record enriched GO BP terms for Group1&Group3 genes in 9-Square

bp14

a list record enriched GO BP terms for Group1&Group4 genes in 9-Square

bp23

a list record enriched GO BP terms for Group2&Group3 genes in 9-Square

bp24

a list record enriched GO BP terms for Group2&Group4 genes in 9-Square

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

See Also

SquareView

EnrichSquare

# Read beta score from gene summary table in MAGeCK MLE results


[Package MAGeCKFlute version 1.0.1 Index]