README.md

In coriell-research/pgx: Pharmacogenomic Allele Predictions

pgx for Predicting PGx Haplotypes

The goal of this package is to use phased VCF data to assign haplotypes to samples for PGx alleles using existing frameworks from the Bioconductor ecosystem.

Data Sources

Reference alleles and haplotype definitions are extracted from PharmVar v5.1.14 database.

Installation

This package is not yet functional but the development version can be installed with:

devtools::install_github("coriell-research/pgx")

Example Usage

library(pgx)


# Use 1kGP VCF file as example (.tbi index must be located in same directory)
vcf_file <- "1kGP_high_coverage_Illumina.chr22.filtered.SNV_INDEL_SV_phased_panel.vcf.gz"

# Read in PGx data for CYP2D6
p <- readPGx(vcf_file, gene = "CYP2D6")

# Display Class information
p
>Class: PGx
>PGx gene: CYP2D6 
>Number of samples: 3202 
>Number of Positions in the Reference: 353 
>Number of Positions in VCF present in Reference: 171 
>Number of Positions in VCF not in Reference: 158

coriell-research/pgx documentation built on June 4, 2022, 11:08 a.m.