xSNPlocations | R Documentation

## Function to extract genomic locations given a list of SNPs

### Description

`xSNPlocations` is supposed to extract genomic locations given a list of SNPs.

### Usage

    xSNPlocations(data, GR.SNP = c("dbSNP_GWAS", "dbSNP_Common"), verbose =
    T,
    RData.location = "http://galahad.well.ox.ac.uk/bigdata")

### Arguments

`data` | a input vector containing SNPs. SNPs should be provided as dbSNP ID (ie starting with rs). Alternatively, they can be in the format of 'chrN:xxx', where N is either 1-22 or X, xxx is genomic positional number; for example, 'chr16:28525386'
`GR.SNP` | the genomic regions of SNPs. By default, it is 'dbSNP_GWAS', that is, SNPs from dbSNP (version 146) restricted to GWAS SNPs and their LD SNPs (hg19). It can be 'dbSNP_Common', that is, Common SNPs from dbSNP (version 146) plus GWAS SNPs and their LD SNPs (hg19). Alternatively, the user can specify the customised input. To do so, first save your RData file (containing an GR object) into your local computer, and make sure the GR object content names refer to dbSNP IDs. Then, tell "GR.SNP" with your RData file name (with or without extension), plus specify your file RData path in "RData.location". Note: you can also load your customised GR object directly
`verbose` | logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display
`RData.location` | the characters to tell the location of built-in RData files. See `xRDataLoader` for details

### Value

an GR oject, with an additional metadata column called 'variant_id' storing SNP location in the format of 'chrN:xxx', where N is either 1-22 or X, xxx is genomic positional number.

### Note

none

### See Also

`xRDataLoader`

### Examples

    ## Not run:
    # Load the XGR package and specify the location of built-in data
    library(XGR)

    ## End(Not run)
    RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev"

    ## Not run:
    # a) provide the seed SNPs with the significance info
    ## load ImmunoBase
    ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase',
    RData.location=RData.location)
    ## get lead SNPs reported in AS GWAS and their significance info (p-values)
    gr <- ImmunoBase$AS$variant
    data <- names(gr)

    # b) define nearby genes
    snp_gr <- xSNPlocations(data=data, RData.location=RData.location)

    ## End(Not run)