ApplyPolygenicScore (version 4.0.1)

combine.vcf.with.pgs: Combine VCF with PGS

Description

Match PGS SNPs to corresponding VCF information by genomic coordinates or rsID using a merge operation.

Usage

combine.vcf.with.pgs(vcf.data, pgs.weight.data)

Value

A list containing a data.table of merged VCF and PGS data and a data.table of PGS SNPs missing from the VCF.

A primary merge is first performed on chromosome and base pair coordinates. For SNPs that could not be matched in the first mergs, a second merge is attempted by rsID if available. This action can account for short INDELs that can have coordinate mismatches between the PGS and VCF data. The merge is a left outer join: all PGS SNPs are kept as rows even if they are missing from the VCF, and all VCF SNPs that are not a component of the PGS are dropped. If no PGS SNPs are present in the VCF, the function will terminate with an error.

Arguments

vcf.data

A data frame/table containing VCF data. Required columns: CHROM, POS.

pgs.weight.data

A data frame/table containing PGS data. Required columns: CHROM, POS.

Examples

# Example VCF
vcf.path <- system.file(
    'extdata',
    'HG001_GIAB.vcf.gz',
    package = 'ApplyPolygenicScore',
    mustWork = TRUE
    );
vcf.import <- import.vcf(vcf.path);

# Example pgs weight file
pgs.weight.path <- system.file(
    'extdata',
    'PGS000662_hmPOS_GRCh38.txt.gz',
    package = 'ApplyPolygenicScore',
    mustWork = TRUE
    );
pgs.import <- import.pgs.weight.file(pgs.weight.path);

merge.data <- combine.vcf.with.pgs(
    vcf.data = vcf.import$split.wide.vcf.matrices$vcf.fixed.fields,
    pgs.weight.data = pgs.import$pgs.weight.data
    );