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affy (version 1.50.0)

makeGoGeneTable: Make Gene table from GO analysis results

Description

A function to create an HTML table showing genes that gave rise to a significant GO term

Usage

makeGoGeneTable(fit.table, probe.sum.table, go.id, cont.name, base.dir = NULL,
  extraname = NULL, probecol = "PROBEID", affy = TRUE)

Arguments

fit.table
The output from topTable
probe.sum.table
The output from running probeSetSummary on a GOHyperGResults object.
go.id
The GO ID of interest
cont.name
The contrast name.
base.dir
Character. Where should the HTML tables be generated? Defaults to NULL.
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

Details

This is an internal function, not intended to be called by the end user. Documentation here for clarity. After running a GO analysis, it is advantageous to output a table listing those genes that gave rise to a significant GO term. This function creates the table, along with links to Netaffx (if the data are Affymetrix) and to the NCBI Gene database (if there are Entrez Gene IDs).