ramwasAnnotateLocations {ramwas} | R Documentation |
Calls biomart annotation database for a vector of locations and assignes the tracks to the locations.
ramwasAnnotateLocations(param, chr, pos)
param |
List of parameters as described in the "RW6_param.Rmd" vignette. |
chr |
A vector of chromosome names or numbers. |
pos |
A vector of genomic locations on the chromosomes. |
This function is used internally by RaMWAS annotation step.
An annotation table, on line per supplied location.
Andrey A Shabalin andrey.shabalin@gmail.com
See vignettes: browseVignettes("ramwas")
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)