rnb.get.mapping

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Description

Gets the mapping information used for a region type. These are structures used to map regions to the genomic loci (or Infinium probes) that target them.

Usage

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rnb.get.mapping(region.type, target.type, assembly = "hg19")

Arguments

region.type

Region type. The built-in types are "cpgislands", "genes", "promoters" and "tiling".

target.type

Target type for sites.

assembly

Genome assembly of interest. See rnb.get.assemblies for the list of supported genomes.

Value

list of mapping structures, one per chromosome. Every mapping structure is an object of type IRanges and stores the range of indices of all sites contained in the respective region. Regions that do not contain sites are left out of the mapping.

Author(s)

Yassen Assenov

Examples

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promoters2probes <- rnb.get.mapping("promoters", "probes450")
promoters2probes[["chr21"]]

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