makeGoGeneTable {affycoretools} | R Documentation |
A function to create an HTML table showing genes that gave rise to a significant GO term
makeGoGeneTable( fit.table, probe.sum.table, go.id, cont.name, base.dir = NULL, extraname = NULL, probecol = "PROBEID", affy = TRUE )
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? |
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).
Returns an HTMLReportRef object.
Jim MacDonald