calculateIncidenceTable: calculateIncidenceTable

In ChristophRau/GSAA: Gene Set Association Analysis

calculateIncidenceTable

Description

Calculates a Gene/GO Term incidence Matrix (equivalent to a SNP Genotype file for a GWAS)

Usage

  calculateIncidenceTable(input,ensembl_dataset="mmusculus_gene_ensembl",mart="illumina_mouseref_8_v2",GO_Member_Threshold=10)

Arguments

input	matrix with gene names as column names, group names as row names, and strengths as entries
ensembl_dataset	Which biomart will be used. Species Specific.
mart	which specific dataset within the biomart will be used. Platform Specific.
GO_Member_Threshold	Threshold for eliminating GO Terms with fewer than this many members from the incidence table (equivalent to a Minor Allele Frequency Filter in a GWAS)

Value

Incidence_Table

The Incidence_Table of genes and GO Terms (equivalent to a genotype file in GWAS)

Author(s)

Christoph Rau

See Also

GSAA,matchkeep

ChristophRau/GSAA documentation built on March 2, 2023, 5:29 a.m.