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", pathway_limit = c(3, 50), adjust = "BH",
  filename = NULL, out.dir = ".", width = 6.5, height = 4, ...)

Arguments

beta

Data frame, with rownames of Entrez IDs, which contains columns of 'group' and 'diff'.

pvalue

Pvalue cutoff.

enrich_method

One of "ORT"(Over-Representing Test) and "HGT"(HyperGemetric test).

organism

"hsa" or "mmu".

pathway_limit

A two-length vector (default: c(3, 50)), specifying the min and max size of pathways for enrichent analysis.

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

go1

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

go2

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

go3

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

go4

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

go13

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

go14

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

go23

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

go24

a list record enriched GO 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

Examples

data(mle.gene_summary)
dd = ReadBeta(mle.gene_summary, organism="hsa")
p = SquareView(dd, ctrlname = "dmso", treatname = "plx")
## Not run: 
 # Read beta score from gene summary table in MAGeCK MLE results
 E1 = EnrichSquare(p$data, organism="hsa")
 print(E1$kegg1$gridPlot)

## End(Not run)

[Package MAGeCKFlute version 1.2.3 Index]