A PHGDataSet Class

A PHGDatSet class is a general class for storing data found within an hVCF file. The main components are:

samples

Sample IDs

reference ranges

start/stop ranges in reference genome

haplotypes

haplotype sequence IDs (MD5 hashes)

metadata

additional information related to haplotype IDs

Prints out information regarding properties from the PHGDataSet class to the console

Usage

# S4 method for class 'PHGDataSet'
show(object)

Arguments

object

A PHGDataSet object

Slots

samples

A character vector of sample identifiers.

refRanges

A GRanges object from the GenomicRanges package representing reference genomic ranges.

hapIds

A matrix of haplotype identifiers.

hapIdMeta

A tibble object containing metadata associated with haplotype identifiers.

hapIdMetaPos

A tibble object containing positional metadata for haplotype identifiers.

dbUri

A character representation of the PHGv2 DB instance