clusterAnnotation: Cluster annotation enrichment scan

In raim/segmenTools: Tools for Functional Genome Exploration

Cluster annotation enrichment scan

Description

Scans for overlap enrichments of a clustering in a matrix of clusterings, potentially simply a TRUE/FALSE table, eg. indicating annotation with a specific Gene Ontology or other term. This input table can be generated eg. with parseAnnotation or parseAnnotationList. The function reports tables of all overlap sizes and their enrichment p-values. The function is a wrapper around clusterCluster, which performs cumulative hypergeometric distribution tests between two clusterings. The result object can be used with sortOverlaps and plotOverlaps.

Usage

clusterAnnotation(
  cls,
  data,
  p = 1,
  cls.srt,
  terms = NULL,
  replace.terms = FALSE,
  bin.filter,
  verbose = TRUE
)

Arguments

cls	a character or numeric vector with the main clustering
data	a string, numeric or logical matrix with other categorizations of genes. Data rows must correspond to clustering in argument cls
p	p-value threshold reporting overlaps
cls.srt	a numeric ar string vector indicating a cluster sorting, allows also to analyze only a subset of clusters in argument cls
terms	optional map of annotation key to descriptions
replace.terms	replace annotation terms by the descriptions in argument terms
bin.filter	string, indicating bins (categories in data) to be globally omitted; useful eg. for logical data to omit all enrichments with category "FALSE" (indicating deprivement)
verbose	print progress messages

raim/segmenTools documentation built on March 20, 2024, 6:23 a.m.