ssdGSA (version 0.1.1)

ssdGSA_individual: Single Sample Directional Gene Set Analysis Using Individual Weighted Scores

Description

This function is to calculate single sample directional (disease weighted) gene set scores for a given disease using individual weighted scores.

Usage

ssdGSA_individual(Data, Gene_sets, Direction_matrix)

Value

Matrix of directional gene set scores with rows corresponding to gene sets and columns corresponding to different samples will be return.

Arguments

Data

Data matrix of gene expressions with gene ensembl ID as row names and columns corresponding to different samples.

Gene_sets

A list of gene sets with gene set names as component names, and each component is a vector of gene entrez ID.

Direction_matrix

Matrix containing directionality information for each gene, such as effect size, t statistics, p value of summary statistics. Each row of the direction matrix is for one gene, and there should be at least two columns (with the 1st column containing gene entrez ID, and 2nd column containing directionality information).

Details

Single sample directional gene set analysis using individual weighted scores inherits the standard gene set variation analysis(GSVA) method, but also provides the option to use summary statistics from any analysis (disease vs healthy, lesional side vs nonlesional side, etc..) input to define the direction of gene sets used for directional gene set score calculation for a given disease. This function is specific for using individual weighted scores.

See Also

ssdGSA

Examples

ssdGSA_individual(Data = data_matrix_entrezID,
                  Gene_sets = gene_sets[c(1,2,4)],
                  Direction_matrix = direction_matrix
                  )