Prepare TORUS input files

Prepares two files necessary for running TORUS: z-score file and annotation file.

prepare_torus_input_files(
  sumstats,
  annotation_bed_files,
  torus_input_dir = "torus_input",
  torus_annot_file = "torus_annotations.txt.gz",
  torus_zscore_file = "torus_zscore.txt.gz"
)

Arguments

sumstats

A data frame of GWAS summary statistics, with required columns: "snp", "chr", "pos", "locus" and "zscore".

annotation_bed_files

Path to annotation files in BED format. The bed file must have at least three columns: "chr", "start", "end". Chromosomes should be numeric (no "chr").

torus_input_dir

Directory to save TORUS input files.

torus_annot_file

Annotation file name (without path).

torus_zscore_file

z-score file name (without path).

Value

A list containing paths to the z-score file and annotation file.

Examples

if (FALSE) {
torus.files <- prepare_torus_input_files(sumstats, annotation_bed_files)
}