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

### See Also

See vignettes: `browseVignettes("ramwas")`

### 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 1.18.0 Index]