sigPathway (version 1.40.0)

getPathwayStatistics.NGSk: 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

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.

Details

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