R: Extract Biomart Annotation for a Vector of Locations.

ramwasAnnotateLocations {ramwas}

R Documentation

Extract Biomart Annotation for a Vector of Locations.

Description

Calls biomart annotation database for a vector of locations and assignes the tracks to the locations.

Usage

ramwasAnnotateLocations(param, chr, pos)

Arguments

`param`	List of parameters as described in the "RW6_param.Rmd" vignette. Try: `vignette("RW6_param","ramwas")`.
`chr`	A vector of chromosome names or numbers.
`pos`	A vector of genomic locations on the chromosomes.

Details

This function is used internally by RaMWAS annotation step.

Value

An annotation table, on line per supplied location.

Author(s)

Andrey A Shabalin andrey.shabalin@gmail.com

Examples

bihost = "grch37.ensembl.org"
bimart = "ENSEMBL_MART_ENSEMBL"
bidataset = "hsapiens_gene_ensembl"
biattributes = c("hgnc_symbol", "entrezgene", "strand")
bifilters = list(with_hgnc_trans_name = TRUE)
biflank = 0

param = ramwasParameters(
    bihost = bihost,
    bimart = bimart,
    bidataset = bidataset,
    biattributes = biattributes,
    bifilters = bifilters,
    biflank = biflank)

# Test a location
chr = "chr1"
pos =  15975530
## Not run: 
ramwasAnnotateLocations(param, chr, pos)

## End(Not run)

[Package ramwas version 1.6.0 Index]