MergedSNPs.Hsapiens.dbSNP149.GRCh38p7

The goal of MergedSNPs.Hsapiens.dbSNP149.GRCh38p7 is to allow an easy translation map old SNP identifiers to its current SNP id. Note that current means current as of version 149 of dbSNP (which is rather old nowadays).

This data set is based on the columns rsHigh (old SNP identifier) and rsCurrent (new SNP identifier) from the file RsMergeArch.bcp.gz. Note that the link to this file is no longer of the version provided by this package. To inspect the version 149 of RsMergeArch.bcp.gz browse into /data-raw/RsMergeArch.bcp.gz.

Installation

Because I use Git LFS to track some of the files in this R package, you will need to have Git LFS installed before installing this package. You can check if you have Git LFS already installed by running:

git lfs version

It should return Git LFS’s version if installed, or a Git error: git: 'lfs' is not a git command. See 'git --help'.

If you don’t have it installed already, and if you are on Ubuntu, you can install it with:

sudo apt-get update -y
sudo apt-get install -y git-lfs

Then, because of issues #192, #91584, #889, you need to clone this repository first and then install from the local folder generated on your computer:

# This will clone the repository to your home folder.
cd ~
git clone https://github.com/maialab/MergedSNPs.Hsapiens.dbSNP149.GRCh38p7

And finally install MergedSNPs.Hsapiens.dbSNP149.GRCh38p7 from the local folder (assuming it’s in your home folder):

# install.packages("remotes")
remotes::install_local("~/MergedSNPs.Hsapiens.dbSNP149.GRCh38p7")

If the installation went successful, you may remove the local folder ~/MergedSNPs.Hsapiens.dbSNP149.GRCh38p7 (or other path if you cloned to another folder):

rm -rf ~/MergedSNPs.Hsapiens.dbSNP149.GRCh38p7

Usage

Please note that the SNP identifiers should be integer numbers, and hence without the "rs" prefix.

library(MergedSNPs.Hsapiens.dbSNP149.GRCh38p7)

snps <- as.numeric(253020:253050)
current_snp(snps)
#>  [1] 252966 252967 252968 252969 252970 252971 252972 252973 252974 252975
#> [11] 252976 252977 252978 252979 252980 252981 252982 253037 252959 252960
#> [21] 252961 253041 252963 252964 252965 253045 253046 250716 250718 250719
#> [31] 250721

If you rather have those SNPs that are not found in the translation table returned as NA, then do this instead:

current_snp(snps, keep.orig.snp.if.not.merged = FALSE)
#>  [1] 252966 252967 252968 252969 252970 252971 252972 252973 252974 252975
#> [11] 252976 252977 252978 252979 252980 252981 252982     NA 252959 252960
#> [21] 252961     NA 252963 252964 252965     NA     NA 250716 250718 250719
#> [31] 250721