makeGoTable: Create HTML tables for Gene Ontology (GO) analyses

Description

This function is used to create HTML tables to present the results from a Gene Ontology (GO) analysis.

Usage

makeGoTable(fit.table, go.summary, probe.summary, cont.name,
  base.dir = "GO_results", extraname = NULL, probecol = "PROBEID",
  affy = TRUE)

Arguments

fit.table

The output from topTable

go.summary

The output from running summary on a GOHyperGResults object.

probe.summary

The output from running probeSetSummary on a GOHyperGResults object.

cont.name

The contrast name.

base.dir

Character. Where should the HTML tables be generated? Defaults to GO_results.

extraname

Character. An extra name that can be used if the contrast name isn't descriptive enough.

probecol

The column name in the topTable object that contains probe IDs. Defaults to PROBEID.

affy

Boolean. Are the arrays from Affymetrix?

Value

Returns an HTMLReportRef object, which can be used when creating an index page to link to the results.

Details

After running a GO analysis, it is often useful to first present a table showing the set of significant GO terms for a given comparison, and then have links to a sub-table for each GO term that shows the genes that were responsible for the significance of that term. The first table can be generated using the summary function, but it will not contain the links to the sub-table. The ReportingTools package has functionality to make these tables and sub-tables automatically, but the default is to include extra glyphs in the main table that are not that useful.

This function is intended to generate a more useful version of the table that one normally gets from ReportingTools.