geneset_VIF: Compute Variance Inflation Factors for gene sets

In CBMR-Single-Cell-Omics-Platform/SCOPfunctions: Single Cell Omics Platform Functions

Description

Utility function to compute Variance Inflation Factors for gene sets using an expression dataset in order to account for inter-gene correlation in gene sets derived from expression data

Usage

geneset_VIF(datExpr, list_genesets, min_feats_present = 5)

Arguments

datExpr	gene * cell expression matrix with row and column names
list_genesets	list of genesets, using same gene names as datExpr
min_feats_present	a minimum number of features shared between mat_datExpr and vec_geneWeights

Value

list of 2-vectors, one per geneset. First vector element is VIF, second is mean Pearson's rho correlation.

References

modified from https://rdrr.io/bioc/qusage/src/R/qusage.R . drawing on https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458527/

CBMR-Single-Cell-Omics-Platform/SCOPfunctions documentation built on May 29, 2021, 3:52 p.m.