prepare_torus_input_files: Prepare TORUS input files

In kevinlkx/Mapgen: Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Prepare TORUS input files

Description

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

Usage

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

## Not run: 
torus.files <- prepare_torus_input_files(sumstats, annotation_bed_files)

## End(Not run)

kevinlkx/Mapgen documentation built on April 2, 2024, 5:48 a.m.