getPathwayStatistics {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(tab, phenotype, G, index, ngroups = 2,
                         statList = NULL, keepUnknownProbes = FALSE,
                         annotpkg = NULL)

### Arguments

`tab` | a numeric matrix of expression values, with the rows and columns representing probe sets and sample arrays, respectively
`phenotype` | a numeric (or character if `ngroups` >= 2) vector indicating the phenotype
`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`
`ngroups` | an integer indicating the number of groups in the expression matrix
`statList` | a list containing results from `calcTStatFast`
`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 mean, standard deviation, and 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, mean, standard deviation, the test statistic (e.g., t-test), and the corresponding unadjusted p-value.
If `ngroups` = 1, the Pearson correlation coefficient is also returned.
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 of `calculate.NTk` or `calculate.NEk` for example code that uses `getPathwayStatistics`

### Author(s)

Weil Lai

[Package sigPathway version 1.12.1 Index]