Skip to contents

Helper function to build HaplotypeGraph object

Source: R/class_haplotype_graph.R
buildHaplotypeGraph.Rd

Creates a HaplotypeGraph object to be used to build and store an rJava reference object pointing to a HaplotypeGraph object from the PHG API.

Usage

buildHaplotypeGraph(
  phgMethodObj,
  chrom = NULL,
  includeSequence = FALSE,
  includeVariants = FALSE
)

Arguments

phgMethodObj

A PHGMethod object.

chrom

A vector of chromosomes to include in graph. If NULL, defaults to all. To specify multiple chromosome, pass as a vector of strings (i.e. c("1", "2", "3")). Is currently only used for haplotypes.

includeSequence

Whether to include sequences in haplotype nodes. Is currently only used for haplotypes. NOTE: this will greatly increase memory consumption!

includeVariants

Whether to include variant contexts in haplotype nodes. Is currently only used for haplotypes. NOTE: this will greatly increase memory consumption!