Infer genome builds

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

get_genome_builds(
  sumstats_list,
  header_only = TRUE,
  sampled_snps = 10000,
  names_from_paths = FALSE,
  dbSNP = 155,
  nThread = 1
)

Arguments

sumstats_list

A named list of paths to summary statistics, or a named list of data.table objects.

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.

sampled_snps

Downsample the number of SNPs used when inferring genome build to save time.

names_from_paths

Infer the name of each item in sumstats_list from its respective file path. Only works if sumstats_list is a list of paths.

dbSNP

version of dbSNP to be used (144 or 155). Default is 155.

nThread

Number of threads to use for parallel processes.

Value

ref_genome the genome build of the data

Details

Iterative version of get_genome_build.

Examples

# Pass path to Educational Attainment Okbay sumstat file to a temp directory

eduAttainOkbayPth <- system.file("extdata", "eduAttainOkbay.txt",
    package = "MungeSumstats"
)
sumstats_list <- list(ss1 = eduAttainOkbayPth, ss2 = eduAttainOkbayPth)

## Call uses reference genome as default with more than 2GB of memory,
## which is more than what 32-bit Windows can handle so remove certain checks
is_32bit_windows <-
    .Platform$OS.type == "windows" && .Platform$r_arch == "i386"
if (!is_32bit_windows) {
    
    #multiple sumstats can be passed at once to get all their genome builds:
    #ref_genomes <- get_genome_builds(sumstats_list = sumstats_list)
    #just passing first here for speed
    sumstats_list_quick <- list(ss1 = eduAttainOkbayPth)
    ref_genomes <- get_genome_builds(sumstats_list = sumstats_list_quick,
                                     dbSNP=144)
}
#> Inferring genome build of 1 sumstats file(s).
#> Inferring genome build.
#> Reading in only the first 10000 rows of sumstats.
#> Importing tabular file: /__w/_temp/Library/MungeSumstats/extdata/eduAttainOkbay.txt
#> Checking for empty columns.
#> Standardising column headers.
#> First line of summary statistics file: 
#> MarkerName	CHR	POS	A1	A2	EAF	Beta	SE	Pval	
#> Loading SNPlocs data.
#> Loading reference genome data.
#> Preprocessing RSIDs.
#> Validating RSIDs of 93 SNPs using BSgenome::snpsById...
#> BSgenome::snpsById done in 12 seconds.
#> Loading SNPlocs data.
#> Loading reference genome data.
#> Preprocessing RSIDs.
#> Validating RSIDs of 93 SNPs using BSgenome::snpsById...
#> BSgenome::snpsById done in 42 seconds.
#> Inferred genome build: GRCH37
#> Time difference of 55.81949 secs
#> GRCH37: 1 file(s)