getPathwayStatistics: Give the statistics for the probe sets in a pathway
In sigPathway: Pathway Analysis

Description Usage Arguments Details Value Note Author(s)

Gives the statistics for the probe sets associated with a pathway.

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

`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

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

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.

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

Weil Lai

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