hyperG2annaffy {affycoretools} | R Documentation |
Output HTML tables containing the 'enriched' genes for each GO term
resulting from a call to hyperGtable
.
hyperG2annaffy(probids, lib, eset, fit = NULL, subset = NULL, comp = 1, type = "MF", pvalue = 0.05, min.count = 10)
probids |
A vector of Affymetrix probe IDs |
lib |
An annotation package (e.g., hgu95av2 ) |
eset |
An ExpressionSet |
fit |
An lmFit object. Only necessary if
statistics are desired in the resulting table. Defaults to NULL . |
subset |
A numeric vector used to select GO terms to output (see
description for more information). Defaults to NULL |
comp |
Which contrast/parameter estimate should be used to
extract the relevant statistics? Only used if fit is not
NULL . See description for more information. |
type |
One of "MF", "CC", "BP", indicating molecular function, cellular component, or biological process, respectively. |
pvalue |
The significance level used to choose GO terms |
min.count |
The minimum number of a given GO term that must be on the chip in order to choose that GO term. This protects against very low p-values that result from the situation where there are very few genes with a given GO term on the chip, but one or two are found in the set of significant genes. |
This function is used to create HTML tables based on the output of
hyperGtable
. The basic idea is as follows; as part of an
analysis, say hyperGtable
was used to create a table of
'enriched' GO terms. Unfortunately, the table only lists GO terms and
the number of probesets that are annotated to those GO terms, and the
client may be interested in knowing what probesets are enriched for
each (or some) GO term.
The default behaviour is to output an HTML table for each GO term,
containing the probesets that are annotated at that term (and that are
in the set of significant genes). If only some of the GO terms are of
interest, one may use the subset
argument to select only
particular rows. In addition, if the relevant t-statistics, p-values
and fold changes are of interest, one can also use the fit
argument to point to an lmFit
object that contains
these data, as well as the comp
argument to indicate which
parameter or contrast to use. Note that the comp
argument
defaults to 1, so the first parameter or contrast will be extracted by default.
This function is used only for the side effect of creating HTML tables.
James W. MacDonald <jmacdon@med.umich.edu>