Function to extract genomic locations given a list of SNPs
xSNPlocations is supposed to extract genomic locations given a
list of SNPs.
1 2 3
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'
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
logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display
the characters to tell the location of built-in
RData files. See
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
## Not run: # Load the XGR package and specify the location of built-in data library(XGR) RData.location <- "http://galahad.well.ox.ac.uk/bigdata_dev" # 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)
Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.