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Import a chunk of the snarl genotypes for a queried region

import_genotype_chunk.Rd

Import a slice of the snarl genotype file (sorted, bgzipped and indexed with Tabix). For each snarl, a table with sample and allele counts is return in a list, along with other information about the snarl.

Usage

import_genotype_chunk(
  genotype_file,
  chrom,
  start_offset,
  end_offset,
  keep_nonvariant = FALSE,
  long_format = FALSE
)

Arguments

genotype_file

path to the snarl genotype file (sorted and indexed with tabix)

chrom

chromosome name

start_offset

start position

end_offset

end position

keep_nonvariant

should we keep variants with only one allele present? Default FALSE.

long_format

should the table we returned in long form. Default FALSE.

Value

a list of snarls with some information (boundary nodes) and the genotype table

Details

The list returned as one element per snarl. Each snarl element has a *GT* data.frame with a *sample* column and a column for each alelle (in the form al0, al1, etc). Each row in this *GT* data.frame correspond to a sample and inform each allele's count. That table could be combined with the phenotype and used for a regression test, for example.