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)

Arguments

tab a numeric matrix of expression values, with the rows and columns representing probe sets and sample arrays, respectively
phenotype a numeric 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

Details

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

Value

A data frame indicating the 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.

Note

See the help page for calculate.NTk or calculate.NEk for example code that uses getPathwayStatistics

Author(s)

Weil Lai


[Package sigPathway version 1.1-0 Index]