gostats: Obtain Gene Ontology (GO) results for a gene list

In moosik/snorm: Supporting function for supervised exploration of data structure

Description

This function performs Gene Ontology analysis on a list of gene. It obtains MF, BP and CC categories for a gene list, calculates enrichment P value and multiple testing correction based on Bonferroni method. Finally for each MF, BP and CC it selects only the categories for which corrected P value is less or equal to 0.05. Returns a data frame with GO categories.

Usage

gostats(data, background, annotation)

Arguments

data	a vector of ENTREZ Gene IDs.
background	a vector ENTREZ Gene IDs used as the universe for the hypergeometric calculation, also ENTREZ Gene IDs.
annotation	- a string giving the name of the annotation data package with GO annotation. See GOHyperGParams-class.

Value

data frame object with GO results. Columns: Ontology (MF, BP or CC), GOID, Pvalue, OddsRatio, ExpCount, Count, Size, Term, P.Bonferroni

See Also

fs

moosik/snorm documentation built on May 23, 2019, 6:11 a.m.