PGx-class: PGx class object
In coriell-research/pgx: Pharmacogenomic Allele Predictions

PGx-class

R Documentation

PGx class object

Description

The PGx class inherits from VCF. Like the CollapsedVCF class it is expected that users will not create instances of the PGx class but instead the PGx class will be created by one of the constructor functions, i.e. readPGx.

The 'gene' slot of a PGx object contains the gene name of the gene for which the PGx locations were extracted from the input VCF.

The 'referencePositions' slot of a PGx object contains a GRanges object of the reference PGx positions that were used to subset the input VCF file

The 'missingPositions' slot of a PGx object contains a GRanges object of any position missing from the input VCF file that is present in the reference PGx dataset.

The 'matchingPositions' slot of a PGx object contains a GRanges object of any position that has a matching location with the reference PGx dataset.

The 'referenceHaplotypes' slot of a PGx object contains a GRanges object of the positions used to subset the VCF. These positions define the reference PGx alleles.

Usage

## S4 method for signature 'PGx'
show(object)

## S4 method for signature 'PGx'
gene(x)

## S4 method for signature 'PGx'
referencePositions(x)

## S4 method for signature 'PGx'
missingPositions(x)

## S4 method for signature 'PGx'
matchingPositions(x)

## S4 method for signature 'PGx'
referenceHaplotypes(x)

Value

Name of the PGx gene

GRanges object

Slots

gene: The PGx gene used to construct the PGx object. See pgxGenes() for available genes.
referencePositions: GRanges object containing all unique allele positions for the reference gene.
missingPositions: GRanges object containing all positions in the reference that are missing from the input VCF.
matchingPositions: GRanges object containing all positions in the reference that have matches in the input VCF.
referenceHaplotyes: GRanges object containing all positions for all alleles ans suballeles for the reference gene.