makeGoGeneTable: Make Gene table from GO analysis results
In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

makeGoGeneTable

R Documentation

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?

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).