get_compound_hetz_ko: get compound heterozygous knockouts

In frhl/our: genetic data analysis

Description

manually open the phased GT of each individual in the context of a gene, to figure out which one are compound hetz. todo: rework for smarter, less laborious. todo: also allow single homozygous (trans) variants

Usage

get_compound_hetz_ko(
  vcf,
  vcf.col.chr = NULL,
  vcf.col.rsid = NULL,
  ref,
  ref.col.chr = NULL,
  ref.col.rsid = NULL,
  ref.col.gene = NULL,
  ref.col.info = NULL,
  verbose = T,
  verbose.iter = 10000
)

Arguments

vcf	a phased vcf file.
vcf.col.chr	integer. column for chromosome.
vcf.col.rsid	integer.
ref	a reference file with at least the follwoing columns: chr, bp, rsid, gene
ref.col.chr	integer.
ref.col.rsid	integer.
ref.col.gene	gene.
ref.col.info	info column wheree entries are seperated by '|'
verbose	boolean.
verbose.iter	how often should iter be printed.

Note

VCF is expected to have a header. Thus, use fwrite(.., header = T).

frhl/our documentation built on Feb. 5, 2021, 7:30 p.m.