Check genome build

If fullSS_genome_build==NULL and munged=TRUE, infers genome build (hg19 vs. hg38) from summary statistics using get_genome_builds. This can only be done with summary statistics that have already been munged by format_sumstats. When fullSS_genome_build is a synonym of hg19 or hg38, this function simply returns a standardized version of the user-provided genome build.

check_genome(
  fullSS_genome_build = NULL,
  munged = FALSE,
  fullSS_path = NULL,
  sampled_snps = 10000,
  names_from_paths = TRUE,
  dbSNP = 155,
  nThread = 1,
  verbose = TRUE
)

Arguments

fullSS_genome_build

Genome build of the full summary statistics (fullSS_path). Can be "GRCH37" or "GRCH38" or one of their synonyms.. If fullSS_genome_build==NULL and munged=TRUE, infers genome build (hg19 vs. hg38) from summary statistics using get_genome_builds.

munged

Whether fullSS_path have already been standardised/filtered full summary stats with format_sumstats. If munged=FALSE you'll need to provide the necessary column names to the colmap argument.

fullSS_path

Path to the full summary statistics file (GWAS or QTL) that you want to fine-map. It is usually best to provide the absolute path rather than the relative path.

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 parallelise saving across.

verbose

Print messages.

Value

Character string indicating genome build.

Examples

fullSS_path <- echodata::example_fullSS()
#> Writing file to ==> /tmp/Rtmp0dbVNr/nalls2019.fullSS_subset.tsv
build <- check_genome(fullSS_genome_build="hg19",
                      fullSS_path=fullSS_path)