getSearchSpace: getSearchSpace

In aertslab/ScoMAP: ScoMAP: Single-Cell Omics Mapping into spatial Axes using Pseudotemporal ordering

Description

Get regions per gene in which to look for potential enhancers to be linked

Usage

getSearchSpace(txdb, org.db, genes, extend = c(50000, 50000))

Arguments

txdb	Txdb object matching with the genome assembly used for the analysis
org.db	Org.Db objet for the corresponding species
genes	Genes for which enhancer-to-gene links want to be inferred
extend	Space around the TSS that must be considered (first value, upstream; second, downstream TSS). In addition, intronic regions in the gene will be considered. Default=c(50000, 50000)

Value

Genomic ranges object containing the regions considered for each gene (as metadata)

Examples

searchSpace <- getSearchSpace(txdb, org.db, rownames(DGEM), extend=c(50000, 50000))

aertslab/ScoMAP documentation built on Oct. 8, 2021, 1:15 a.m.