rnaCentralGenomicCoordinatesSearch: Retrieves annotated non-coding RNA in a set of genomic ranges

In LaraSellesVidal/ncRNAtools: An R toolkit for non-coding RNA

Description

Retrieves RNAcentral entries corresponding to non-coding RNA present within a specified set of genomic coordinates

Usage

rnaCentralGenomicCoordinatesSearch(genomicRanges, species)

Arguments

genomicRanges

GRanges object specifying the genomic coordinates for which known non-coding RNA should be retrieved. Each sequence name must be of the format chr? or simply ?, where ? can be any number or the "X" or "Y" characters. These denote, respectively, standard somatic chromosomes and sexual chromosomes. Additionally, sequence name can also be "MT", which refers to the mitochondrial DNA. Multiple ranges can be provided in the same GRanges object, but they must all belong to the same organism.

species

string specifying the species to which the ranges supplied with the genomicRanges argument refer. The scientific name should be provided. The list of species for which search of RNAcentral by genomic coordinates is supported can be found at https://rnacentral.org/help/genomic-mapping.

Value

A nested list whose length matches the number of genomic ranges provided through genomicRanges. Each top-level element is a list containing all hits found for a given genomic range. In turn, each of the elements of such list representing a hit is a list comprising the following elements that describe the hit:

rnaCentralID	RNAcentral ID of the non-coding RNA that was identified as a hit
species	species whose genome was searched
description	brief description of the RNA sequence of the hit
RNAType	category of the RNA sequence of the hit
genomicCoordinates	GRanges object containing a single range, within which the hit was found

References

https://rnacentral.org/help/genomic-mapping

https://rnacentral.org/api

Examples

# Generate a GRanges object with 2 genomic ranges specifying coordinates of
# the human genome:

genomicCoordinates <- GenomicRanges::GRanges(seqnames=S4Vectors::Rle(c("chr3", "chr4")),
ranges=IRanges::IRanges(rep(39745816, 2), rep(39847679, 2)))

# Retrieve known annotated non-coding RNA present in the specified genomic
# ranges:

knownNonCodingRNA <- rnaCentralGenomicCoordinatesSearch(genomicCoordinates, "Homo sapiens")

LaraSellesVidal/ncRNAtools documentation built on Oct. 17, 2020, 6:03 a.m.