Make Gene table from GO analysis results

Share:

Description

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

Usage

1
2
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

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.