clusterAnnotation: clustering enrichment scan

Description Usage Arguments

View source: R/clusterTools.R

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. It 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.

Usage

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clusterAnnotation(cls, data, p = 1, cls.srt, terms = NULL, 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

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 Nov. 9, 2018, 5:38 p.m.