Find closest refseq gene

Description

This function is used to find the nearest refseq transcript(s) to a point in the genome specified. Note that it is limited to the refseq transcripts listed at genome.ucsc.edu, where this function goes for information.

Usage

1
findClosestGene(chrom, pos, genome = "hg17", position = "txStart")

Arguments

chrom

Usually specified like 'chr1', 'chr2', etc.

pos

A position in base pairs in the genome

genome

Something like 'hg16', 'hg17', 'mm6', etc.

position

The location to measure distance from: one of 'txStart', 'txEnd', 'cdsStart', 'cdsEnd'

Details

The first time the function is run, it checks to see if the refflat table for the given genome is present in the package environment. If not, it downloads it to the /tmp directory and gunzips it (using getRefflat. It is then stored so that in future calls, there is no re-download required.

Value

A data frame with the gene name, refseq id(s), txStart, txEnd, cdsStart, cdsEnd, exon count, and distance. Note that distance is measured as pos-position, so negative values mean that the point in the gene is to the left of the point specified in the function call (with the p-tel on the left).

Note

The function may return more than one transcript, as several transcripts may have the same start site

Author(s)

Sean Davis <sdavis2@mail.nih.gov>

Examples

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findClosestGene('chr1',100000000,'hg17')