getPathwayStatistics.NGSk {sigPathway} | R Documentation

## Give the statistics for the probe sets in a pathway

### Description

Gives the statistics for the probe sets associated with a pathway.

### Usage

    getPathwayStatistics.NGSk(statV, probeID, G, index,
                              keepUnknownProbes = FALSE, annotpkg = NULL)

### Arguments

`statV` | a numeric vector of test statistic (not p-values) for each individual probe/gene
`probeID` | a character vector containing the names of probe sets associated with a matrix of expression values
`G` | a list containing the source, title, and probe sets associated with each curated pathway
`index` | an integer vector specifying the pathway(s) to summarize in `G`
`keepUnknownProbes` | a boolean indicating whether to keep the names of probe sets not represented in tab in the summary data frame
`annotpkg` | a character vector specifying the name of the BioConductor annotation package to use to fetch accession numbers, Entrez Gene IDs, gene name, and gene symbols

### Details

This function gives the test statistic for each probe in the pathway as indicated in `G[[index]]`.

### Value

A list containing data frames (1 per pathway) with the probes' name and the corresponding test statistic.
If a valid `annotpkg` is specified, the probes' accession numbers, Entrez Gene IDs, gene name, and gene symbols are also returned. This option only works if the probes in the gene set list `G` are manufacturer IDs corresponding to those used in making the BioConductor annotation package.

### Note

See the help page for `calculate.NGSk` for example code that uses `getPathwayStatistics.NGSk`

### Author(s)

Weil Lai

[Package sigPathway version 1.12.1 Index]