The goal of Chr.Rpts.Hsapiens.dbSNP149.GRCh38p7 is to provide dbSNP Chromosome Reports’ data in data frame format. The information made available by this package is the one found in ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b149_GRCh38p7/.
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 versionIt 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-lfsThen, 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/Chr.Rpts.Hsapiens.dbSNP149.GRCh38p7And finally install Chr.Rpts.Hsapiens.dbSNP149.GRCh38p7 from the local folder (assuming it’s in your home folder):
# install.packages("remotes")
remotes::install_local("~/Chr.Rpts.Hsapiens.dbSNP149.GRCh38p7")If the installation went successful, you may remove the local folder
~/Chr.Rpts.Hsapiens.dbSNP149.GRCh38p7 (or other path if you cloned to
another folder):
rm -rf ~/Chr.Rpts.Hsapiens.dbSNP149.GRCh38p7The package contains only one function which is read_chr_rpt. Browse
this function help page (?read_chr_rpt) to know how to use it:
library(Chr.Rpts.Hsapiens.dbSNP149.GRCh38p7)
chrom_Y <- read_chr_rpt('Y')
chrom_Y[1:10, 1:4]
#> snp_id mapweight snp_type chr_hits
#> 1 3894 2 0 1
#> 2 3895 2 0 1
#> 3 3896 2 0 1
#> 4 3897 2 0 1
#> 5 3898 2 0 1
#> 6 3899 2 0 1
#> 7 3900 2 0 1
#> 8 3901 2 0 1
#> 9 3902 2 0 1
#> 10 3903 2 0 1