get_genome_build: Infers the genome build of the summary statistics file...

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

Infers the genome build of the summary statistics file (GRCh37 or GRCh38) from the data. Uses SNP (RSID) & CHR & BP to get genome build.

Description

Infers the genome build of the summary statistics file (GRCh37 or GRCh38) from the data. Uses SNP (RSID) & CHR & BP to get genome build.

Usage

get_genome_build(
  sumstats,
  nThread = 1,
  sampled_snps = 10000,
  standardise_headers = TRUE,
  mapping_file = sumstatsColHeaders,
  dbSNP = 155,
  header_only = FALSE,
  allele_match_ref = FALSE,
  ref_genome = NULL,
  chr_filt = NULL
)

Arguments

sumstats	data table/data frame obj of the summary statistics file for the GWAS ,or file path to summary statistics file.
nThread	Number of threads to use for parallel processes.
sampled_snps	Downsample the number of SNPs used when inferring genome build to save time.
standardise_headers	Run standardise_sumstats_column_headers_crossplatform.
mapping_file	MungeSumstats has a pre-defined column-name mapping file which should cover the most common column headers and their interpretations. However, if a column header that is in your file is missing of the mapping we give is incorrect you can supply your own mapping file. Must be a 2 column dataframe with column names "Uncorrected" and "Corrected". See data(sumstatsColHeaders) for default mapping and necessary format.
dbSNP	version of dbSNP to be used (144 or 155). Default is 155.
header_only	Instead of reading in the entire sumstats file, only read in the first N rows where N=sampled_snps. This should help speed up cases where you have to read in sumstats from disk each time.
allele_match_ref	Instead of returning the genome_build this will return the propotion of matches to each genome build for each allele (A1,A2).
ref_genome	name of the reference genome used for the GWAS ("GRCh37" or "GRCh38"). Argument is case-insensitive. Default is NULL which infers the reference genome from the data.
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

ref_genome the genome build of the data

neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.