getPathwayStatistics: 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

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

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.

Details

This function gives the mean, standard deviation, and test statistic for each probe in the pathway as indicated in G[[index]].