probeSetSummary {GOstats} | R Documentation

## Summarize Probe Sets Associated with a hyperGTest Result

### Description

Given the result of a `hyperGTest` run (an instance of `GOHyperGResult`), this function lists all Probe Set IDs associated with the selected Entrez IDs annotated at each significant GO term in the test result.

### Usage

    probeSetSummary(result, pvalue, categorySize)

### Arguments

`result` | A `GOHyperGResult` instance. This is the output of the `hyperGTest` function when testing the GO category.
`pvalue` | Optional p-value cutoff. Only results for GO terms with a p-value less than the specified value will be returned. If omitted, `pvalueCutoff(result)` is used.
`categorySize` | Optional minimum size (number of annotations) for the GO terms. Only results for GO terms with `categorySize` or more annotations will be returned. If omitted, no category size criteria will be used.

### Details

Usually the goal of doing a Fisher's exact test on a set of significant probesets is to find pathways or cellular activities that are being perturbed in an experiment. After doing the test, one usually gets a list of significant GO terms, and the next logical step might be to determine which probesets contributed to the significance of a certain term.

Because the input for the Fisher's exact test consists of a vector of unique Entrez Gene IDs, and there may be multiple probesets that interrogate a particular transcript, the ouput for this function lists all of the probesets that map to each Entrez Gene ID, along with an indicator that shows which of the probesets were used as input.

The rationale for this is that one might not be able to assume a given probeset actually interrogates the intended transcript, so it might be useful to be able to check to see what other similar probesets are doing.

### Value

A `list` of `data.frame`. Each element of the list corresponds to one of the GO terms (the term is provides as the name of the element). Each `data.frame` has three columns: the Entrez Gene ID (`EntrezID`), the probe set ID (`ProbeSetID`), and a 0/1 indicator of whether the probe set ID was provided as part of the initial input (`selected`)
Note that this 0/1 indicator will only be correct if the 'geneId' vector used to construct the `GOHyperGParams` object was a named vector (where the names are probeset IDs).

### Author(s)

S. Falcon and J. MacDonald

[Package GOstats version 2.2.6 Index]