getSnpIdFromLocation: Get rsIDs from locations of SNP
In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description Usage Arguments Details Value Author(s) Examples

Given a GRanges object of SNPs and a SNPlocs annotation, this function attempts to replace the names of the GRanges object entries with rs-IDs.

getSnpIdFromLocation(GR, ...)

## S4 method for signature 'GRanges'
getSnpIdFromLocation(GR, SNPloc, return.vector = FALSE, verbose = TRUE)

`GR`	A `GRanges` that contains positions of SNPs to look up
`...`	arguments to pass on
`SNPloc`	A `SNPlocs object` containing information on SNP locations (e.g. SNPlocs.Hsapiens.dbSNP.xxxxxxxx)
`return.vector`	Setting `return.vector=TRUE` returns vector with rsIds
`verbose`	Setting `verbose=TRUE` makes function more talkative

This function is used to try to identify the rs-IDs of SNPs in a GRanges object.

getSnpIdFromLocation returns the same GRanges object it was given with, but with updated with rs.id information.

Jesper R. Gadin, Lasse Folkersen

is_32bit_windows <- .Platform$OS.type == "windows" &&
                  .Platform$r_arch == "i386"
if (!is_32bit_windows && require(SNPlocs.Hsapiens.dbSNP144.GRCh37)) {
	#load example data
	data(ASEset)

  #get counts at the three positions specified in GRvariants
  updatedGRanges <- getSnpIdFromLocation(rowRanges(ASEset),
    SNPlocs.Hsapiens.dbSNP144.GRCh37)
}