load_ref_genome_data: Load the reference genome data for SNPs of interest

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Load the reference genome data for SNPs of interest

Description

Load the reference genome data for SNPs of interest

Usage

load_ref_genome_data(
  snps,
  ref_genome,
  dbSNP = c(144, 155),
  msg = NULL,
  chr_filt = NULL
)

Arguments

snps	Character vector SNPs by rs_id from sumstats file of interest.
ref_genome	Name of the reference genome used for the GWAS (GRCh37 or GRCh38)
dbSNP	version of dbSNP to be used (144 or 155)
msg	Optional name of the column missing from the dataset in question. Default is NULL
chr_filt	Internal for testing - filter reference genomes and sumstats to specific chromosomes for testing. Pass a list of chroms in format: c("1","2"). Default is NULL i.e. no filtering.

Value

data table of snpsById, filtered to SNPs of interest.

Source

sumstats_dt <- formatted_example() rsids <- MungeSumstats:::load_ref_genome_data(snps = sumstats_dt$SNP, ref_genome = "GRCH37", dbSNP=144)

neurogenomics/MungeSumstats documentation built on July 17, 2024, 3:14 p.m.