xSNPlocations: Function to extract genomic locations given a list of SNPs

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Description

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

Usage

xSNPlocations(data, GR.SNP = c("dbSNP_GWAS", "dbSNP_Common",
"dbSNP_Single"), 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"

## 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)

XGR documentation built on June 18, 2019, 3:01 p.m.