Write summary statistics or fine-mapping results to VCF/BCF

Creates a VCF object from GWAS summary statistics or fine-mapping results and writes it to disk. Supports bgzipped VCF (.vcf.gz/.vcf.bgz) and BCF (.bcf) output formats via VariantAnnotation and Rsamtools.

Usage

writeSumstatsVcf(x, output_path, sample_name = NULL, ...)

# S4 method for class 'GWASSumStats'
writeSumstatsVcf(x, output_path, sample_name = NULL, ...)

# S4 method for class 'FineMappingResult'
writeSumstatsVcf(x, output_path, sample_name = NULL, ...)

Arguments

x

Input data: a GWASSumStats object, a FineMappingResult object, or a data.frame with columns chrom, pos, ref, alt.

output_path

File path for output. Extension determines format: .vcf.gz or .vcf.bgz for bgzipped VCF, .bcf for BCF, .vcf for uncompressed VCF.

sample_name

Name for the VCF sample column (default: trait name or method name from the S4 object).

...

Additional arguments passed to methods.

Value

Invisible path to the written file.