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

In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

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?

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.

Value

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

Author(s)

Jim MacDonald

jmacdon/affycoretools documentation built on Feb. 25, 2023, 4:51 a.m.