pathwayCrosstalk: pathwayCrosstalk

In hemoshear/pathwayTalk:

pathwayCrosstalk

Description

pathwayCrosstalk

Usage

pathwayCrosstalk(expression_matrix, DEPs, groups, pathways, pathway_alpha)

Arguments

expression_matrix	An matrix of gene expression data where the row names are gene probe identifiers and column names are sample identifiers. For RNAseq data, a matrix of un-normalized integer counts. For microarray data, a matrix of intensity values for gene probes with pre-processing completed, including log2 transformation, normalization, removal of control sequences.
DEPs	A data frame of results for the Fisher's exact tests with a column 'p'. The output of fisherPathwayEnrichment().
groups	A dataframe containing the mappings between sample identifiers ('sample_id', a factor with the reference condition as the first level) and associated treatment conditions ('group'). The sample identifiers must be in the same order as the columns of the count_matrix.
pathways	A named list in which each element is a pathway containing a character vector of the corresponding gene IDs.
pathway_alpha	Significance level for pathways. Pathways where the Fisher's exact test p-value is less than 'pathway_alpha' will be labeled as enriched for the purposes of downstream analyses. @return A matrix of discriminating scores in which each column is a pair of enriched pathways and each row is a sample.

hemoshear/pathwayTalk documentation built on July 16, 2022, 12:09 a.m.