makeGoGeneTable: Make Gene table from GO analysis results

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

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).

Value

Returns an HTMLReportRef object.

Author(s)

Jim MacDonald

affycoretools documentation built on Nov. 8, 2020, 6 p.m.