runGoSeq: runGoSeq

In astatham/GOfish: Fishing for GO terms? SO ARE WE!

Description

runGoSeq

Usage

runGoSeq(de.genes,all.genes,onto,genome,ID,rep=1000,p.adj="BH",adj.p.val=.05,bias.data=NULL)

Arguments

de.genes	List of Differentially expressed IDs to test for GO term enrichment and depletion.
all.genes	List of IDs to use as the background.
onto	Which ontology to test, one of "GO:BP", "GO:MF" or "GO:CC".
genome	Which genome to use e.g. "hg19" - passed into getgo.
ID	Which type of ID e.g. "ensGene"- passed into getgo.
rep	Passed to the argument repcnt in the internal call to goseq
p.adj	Which method of p value adjustment for multiple testing to use - for details see help("p.adjust").
adj.p.val	Which p value to use.
bias.data	Customised background for either 450k methylation data or alternative gene lengths. Should be a named vector of integers.

Value

Select background explicitly for those genes annotated to root term of ontology.

Author(s)

Hugh French

astatham/GOfish documentation built on May 10, 2019, 2:05 p.m.