report_enrichment: Report GO/KEGG analysis.

In xpastor/skima:

Description

Report GO/KEGG analysis.

Usage

report_enrichment(all.cpg, sig = 0.05, collection = "GO", prefix = NULL,
  invisible = T)

Arguments

all.cpg	named vector, with significance or any value to subset significant probes
sig	threshold used to subset the probes. Probes below or equal to the threshold are selected
collection	'GO' or 'KEGG'
prefix	file prefix to write the results. It must point to a valid folder
invisible	a boolean to determine if the output of 'missMethyl::gometh' is returned

Details

This function is a wrapper for the 'gometh' function from 'missMethyl' package that directly writes the results into a folder specified in 'prefix'.

Value

A data frame with a row for each GO or KEGG term and the following columns:

Term	GO term if testing GO pathways
Ont	ontology that the GO term belongs to if testing GO pathways. "BP" - biological process, "CC" - cellular component, "MF" - molecular function.
Pathway	the KEGG pathway being tested if testing KEGG terms.
N	number of genes in the GO or KEGG term
DE	number of genes that are differentially methylated
P.DE	p-value for over-representation of the GO or KEGG term term
FDR	False discovery rate

See Also

missMethyl::gometh

xpastor/skima documentation built on May 16, 2019, 3:25 p.m.