buildHaplotypeGraph: Helper function to build HaplotypeGraph object
In maize-genetics/rPHG: R front-end for the practical haplotype graph

buildHaplotypeGraph

R Documentation

Helper function to build HaplotypeGraph object

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

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

`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!