getPathwayStatistics.NGSk: Give the statistics for the probe sets in a pathway

In sigPathway: Pathway Analysis

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

sigPathway documentation built on Nov. 8, 2020, 5:35 p.m.