GOanalysis: GO and KEGG enrichment analysis

In mariavica/mircomb: An R package for analyzing miRNA-mRNA interactions

Description

GO and KEGG enrichment analysis of mRNAs from selected miRNA-mRNA interactions.

Usage

GOanalysis(obj, type, ontology, pval.cutoff = 0.05,
  dat.sum = obj@info[["dat.sum"]], score.cutoff = NULL, sub.miRNA = NULL,
  exclude.miRNA = NULL, sub.mRNA = NULL, organism = "human", FC = NULL,
  up = FALSE, dw = FALSE, add.miRNA = FALSE)

Arguments

obj	a corObject with a net slot already defined
type	"GO" or "REACTOME"
ontology	If type is "GO", the ontology to be analysed: "BP" (Biological Process), "CC" (Cellular Component) or "MF" (Molecular Function). If the type is "REACTOME", write "REACTOME".
pval.cutoff	maximum p value of selected miRNA-mRNA pairs.
dat.sum	minimum concurrences of the miRNA-mRNA pairs across the database(s) used
score.cutoff	maximum score allowed
sub.miRNA	(optional) character vector, names of the miRNAs to limit the targets.
exclude.miRNA	(optional) character vector, the mRNA targets of these miRNAs will be removed.
sub.mRNA	(optional) character, use only these targets.
FC	(optional) minimum FC for the mRNAs.
up	if TRUE, select only upregulated mRNAs.
dw	if TRUE, select only upregulated mRNAs.
organism	"human" or "mouse".
add.miRNA	if TRUE, add the miRNAs that are regulating the selected mRNAs (only if correlation p-values are computed!)

Value

a corObject, with an item of the GO.results slot added. The item is a data.frame with the named "type:ontology" and with the following columns:

• Ontology: "BP" (Biological Process), "CC" (Cellular Component), "MF" (Molecular Function), "KEGG" or "REACTOME"

• ID: term ID

• Pvalue: p value

• OddsRatio: number of mRNAs found/number of expected mRNAs

• ExpCount: expected number of mRNAs

• Count: number of mRNAs in the selected category

• Size: total number of mRNAs in the selected category

• Term: term name

• fdr: corrected p value with BH method

• genescat: mRNAs in the category

• (optional) miRNAs: miRNAs regulating these mRNAs

References

Falcon S and Gentleman R. Using GOstats to test gene list for GO term association. Bioinformatics, 23(7):257-8, 2007.

Yu G. ReactomePA: Reactome Pathway Analysis. R package version 1.10.1.

See Also

package:GOstats, package:ReactomePA

Examples

data(data.obj)
data.obj<-GOanalysis(data.obj,"GO","MF",pval.cutoff=0.05,dat.sum=1)
head([e-mail][["GO:MF"]])

data.obj<-GOanalysis(data.obj,"KEGG","KEGG",pval.cutoff=0.05,dat.sum=1)
head([e-mail][["KEGG:KEGG"]])

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.