hyperGoutput {affycoretools} | R Documentation |
This function will output various tables containing probesets that are annotated to a particular GO, KEGG, or PFAM term. The tables are based on the results from a call to hyperGtest.
hyperGoutput(hyptObj, eset, pvalue, categorySize, fit = NULL, subset = NULL,comp = 1, output = c("selected", "all", "split"), statistics = c("tstat", "pval", "FC"), html = TRUE, text = TRUE, ...)
hyptObj |
A HyperGResult object, usually produced by a call to
hyperGtest |
eset |
An ExpressionSet object |
pvalue |
The p-value cutoff used for selecting significant GO
terms. If not specified, it will be extracted from the
HyperGResult object |
categorySize |
Number of terms in the universe required for a term to be significant. See details for more information |
fit |
An MArrayLM object, produced from a
call to eBayes |
subset |
Numeric vector used to select particular tables to output. The default is to output tables for all terms. See details for more information |
comp |
Numeric vector of length one, used to indicate which
comparison in the MArrayLM object to use for
extracting relevant statistics. See details for more information |
output |
One of 'selected', 'all', or 'split'. See details for more information |
statistics |
Which statistics to output in the resulting tables. Choices include 'tstat', 'pval', or 'FC', corresponding to t-statistics, p-values, and fold change, respectively |
html |
Boolean. Output HTML tables? Defaults to TRUE |
text |
Boolean. Output text tables? Defaults to TRUE |
... |
Allows end user to pass further arguments. The most
notable would be an anncols argument, passed to
probes2table to control the hyperlinked annotation
columns. See aaf.handler for more information |
This function is designed to be used to output the results from a hypergeometric test for over-represented terms. This function would be used at the end of an analysis such as:
1.) Compute expression values
2.) Fit a model using limma
3.) Output significant probesets using limma2annaffy
4.) Perform hypergeometric test using hyperGtest
At step 4, one can output a list of the over-represented terms using
htmlReport
. One might then be interested in
knowing which probesets contributed to the significance of a particular
term, which is what this function is designed to do.
One argument that can be passed to htmlReport
(and also to hyperGoutput
) is categorySize
, which gives a
lower bound for the number of probesets with a particular term in the
universe. In other words, assume that a particular GO term is annotated
to three probesets on a given chip. If, after doing a t-test to detect
differentially expressed probesets, one of those probesets were found
to be significantly differentially expressed and was then used to do a
hypergeometric test, that GO term would be significant, with a small
p-value. However, this is probably not very strong evidence that the GO
term is actually over-represented, since there were only three to begin
with. By setting categorySize
to a sensible value (such as 10),
this situation can be avoided.
This function will output HTML and/or text tables containing annotation
information about each probeset as well as the expression values. In
addition, if limma were used to fit the model, the relevant statistics
(t-statistic, p-value, fold change) can also be output in the table by
passing the MArrayLM
object that resulted from a
call to eBayes
. The statistics
argument can
be used to control which statistics are output.
By default hyperGoutput
will output tables for all significant
terms, which may end up being quite a few tables. Usually only a few
terms are of interest, so there is a subset
argument that can be
used to select only those terms. This argument follows directly from
the order of the table output by htmlReport
or
summary
. For instance, if the first, third and
fifth terms in the HTML table output by
htmlReport
were of interest, one would use
subset=c(1,3,5).
One critical step prior to the hypergeometric test is to subset the
probesets to unique Entrez Gene IDs. It should be noted however, that
the functions used by hypergOutput
will output all the probesets
annotated to a particular term. The output
argument is used to
control this behavior. If output = "selected" (the default), then only
those probesets that correspond to the original subsetting will be
output. If output = "all", then all probesets will be output (grouped
by Entrez ID), with the
'selected' probeset first. If output = "split", then all the probesets
will be output, with all the 'selected' probesets first, followed by
the other probesets, grouped by Entrez ID.
Note that this functionality is reliant on the probesets being
subsetted in a manner that keeps the probeset ID appended to the Entrez
Gene ID. This can be accomplished by using either
findLargest
or getUniqueLL
.
This function returns no value, and is called solely for the side effect of outputting HTML and/or text tables.
James W. MacDonald <jmacdon@med.umich.edu>
hyperGTest
,
htmlReport
, probeSetSummary