filterGenes: Filter Genes by their Genome Features

In jlaffy/infercna: Infer Copy Number Alterations And Clonality In (Single-Cell) RNA-seq Data

Filter Genes by their Genome Features

Description

Filter genes to keep (the default) or to out according to genomic features. For example, filter genes that are either on chromosome 7 or chromosome arm 2p.

Usage

filterGenes(x, value, attribute, out = F)

Arguments

x	a character vector of gene names or a matrix with gene row names.
value	a value or a list of values that are the genome features to filter
attribute	the name(s) of the genome feature(s) in question. One of 'chr', 'arm'.
out	boolean value indicating whether the filtered genes should be thrown rather than kept. Default: F

Value

filtered vector or a matrix with filtered rows, depending on class of <x>.

Examples

 m = useData()
 filterGenes(m, 7, 'chr')
 filterGenes(rownames(m), 7, 'chr')
 filterGenes(m, list(7, c('2p', '3q')), c('chr', 'arm'))

jlaffy/infercna documentation built on Jan. 26, 2024, 11:24 p.m.