Check genome build — check_genome • echolocatoR

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.

Usage

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

## When the build is already known, simply standardizes the name
build <- check_genome(fullSS_genome_build = "hg19")
print(build)
#> [1] "GRCH37"