GO-methods: Odds Ratio Analysis

In ericaenjoy3/GOplot: GO Enrichment Test and Clustering

Description

Odds ratio and P value are computed from fisher.test.

Usage

GO(gclus.obj, gset.obj, filterPADJ = TRUE, filterOR = TRUE,
  Padj.cutoff = 0.05)

## S4 method for signature 'gclus,gset'
GO(gclus.obj, gset.obj, filterPADJ = TRUE,
  filterOR = TRUE, Padj.cutoff = 0.05)

Arguments

gclus.obj	A gclus object.
gset.obj	A gset object.
filterPADJ	Logical, whether to filter with a P value threshold set by Padj.cutoff.
filterOR	Logical, whether to filter out infinite ORs.
Padj.cutoff	Numeric, specififying significance cutoff on adjust P value.

Details

See fisher.test. An alternative and slower approach is to compute odds ratio by a contingency table and estiamte P value from repeated reshuffle analysis.

Value

A list with two entries go_res.obj and go_set.obj.

Examples

## Not run: 
library(GOplot)
gset.obj <- selDB(major="C2.CP", minor="Reactome", type="symbols", species="mouse")
gclus.obj <- new("gclus", tbl=tibble:::as_tibble(data.frame( gene = c("Nanog","Rpl3","Rpl4","Mbl2","Ubr1","Herc2","Asb4","Rnf123","Klf4","Uba5"), clus = factor(c(rep(1,6),rep(2,4))) )) )
res.list <- GO(gclus.obj, gset.obj, filterPADJ=FALSE, filterOR=TRUE)
go_set.obj <- res.list$go_set.obj
go_res.obj <- res.list$go_res.obj
write_GO(go_set.obj, go_res.obj, 'output_txt')
simi(go_set.obj, go_res.obj, 'output_fig')

## End(Not run)

ericaenjoy3/GOplot documentation built on May 6, 2019, 9:50 p.m.