nearestTSS: Find Nearest Transcriptional Start Site

In edgeR: Empirical Analysis of Digital Gene Expression Data in R

Description

Find nearest TSS and distance to nearest TSS for a vector of chromosome loci.

Usage

nearestTSS(chr, locus, species="Hs")

Arguments

chr	character vector of chromosome names.
locus	integer or numeric vector of genomic loci, of same length as chr.
species	character string specifying the species. Possible values include "Hs" (human), "Mm" (mouse), "Rn" (rat), "Dm" (fly) or "Pt" (chimpanzee), but other values are possible if the corresponding organism package is available. See alias2Symbol for other possible values.

Details

This function takes a series of genomic loci, defined by a vector of chromosome names and a vector of genomic positions within the chromosomes, and finds the nearest transcriptional start site (TSS) for each locus. The chromosome names can be in the format "1","2","X" or can be "chr1","chr2","chrX".

This function uses the Bioconductor organism package named "org.XX.eg.db" where XX is species.

Value

A data.frame with components:

gene_id	character vector giving the Entrez Gene ID of the nearest TSS for each element of chr and locus.
symbol	character vector of gene symbols.
strand	character vector with "+" for positive strand genes and "-" for negative strand genes.
tss	integer vector giving TSS.
width	integer vector giving genomic width of the gene.
distance	integer vector giving distance to nearest TSS. Positive values means that the TSS is downstream of the locus, negative values means that it is upstream. Gene body loci will therefore have negative distances and promotor loci will have positive.

Author(s)

Gordon Smyth

See Also

nearestReftoX

Examples

nearestTSS(chr = c("1","1"), locus = c(1000000,2000000))

Example output

Loading required package: limma
      gene_id symbol width     tss strand distance
21087   57801   HES4  1211 1000172      -     -172
24858   85452 CFAP74 81887 2003837      -    -3837

edgeR documentation built on Jan. 16, 2021, 2:03 a.m.