single_component_enrichment: Calculate enrichment for a set of genes in a single component

In MyersGroup/testisAtlas: testisAtlas: R functions and analysis scripts used in the analysis of testis single cell RNAseq

Description

Calculate enrichment for a set of genes in a single component

Usage

single_component_enrichment(gene_vector = SDAresults$loadings[[1]][1, ],
  genes = Mybl1_genes, pos = T, threshold = 200, bg_genes = NULL,
  test = "fisher")

Arguments

genes	character vector of gene set to look for enrichment for
pos	logical; if TRUE (default) the positive gene loadings are ranked highest
threshold	numeric; how many genes should be included in the top genes list used to calculate enrichment
bg_genes	which genes to use as the 'background' default uses all genes in the SDAresults object from SDA
test	string, either binomial (from Exact::exact.test, slow) or fisher (R's fisher.test)
component	number or name of component
factorisation	SDA factorisation object, output of SDAtools::load_results()

Details

Calculate p value of enrichemnt (fishers test) in a component, given a set of genes see component_enrichment for a function to run on all components

MyersGroup/testisAtlas documentation built on Nov. 29, 2020, 9:21 p.m.