goReport: Text report from the 'hyperGTest' function

In EMA: Easy Microarray Data Analysis

Description

Create a text report with the significant probesets for each significant GO category from the result of a call to 'hyperGTest'

Usage

goReport(hgOver, fileout = "report.txt", type = c("CC", "MF", "BP"),
pack.annot, pvalue = 0.05, categorySize=1)

Arguments

hgOver	result from a call to 'hyperGTest'
fileout	name of txt file, by default "report.txt"
type	type of GO categories, by default = c("CC", "MF", "BP")
pack.annot	the annotation package to use
pvalue	cutoff for significant pvalue, by default 0.05
categorySize	integer, minimum size for category, by default = 1

Details

goReport needs packages GOstats and GO.db from Bioconductor.

Value

Txt report with the results of a call to 'hyperGTest'

Author(s)

Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe

See Also

hyperGTest, runHyperGO

EMA documentation built on March 26, 2020, 8:40 p.m.