mapRecomb: Map meiotic recombination events in a single family trio...

In daewoooo/StrandPhaseR: Phase template strands from Strand-seq data

Map meiotic recombination events in a single family trio [father-mother-child].

Description

This function takes as an input phased VCF files for each member of a family trio and maps breakpoints of meiotic recombination in each inherited parental homolog.

Usage

mapRecomb(
  parent1 = NULL,
  parent2 = NULL,
  child = NULL,
  genome = "hg38",
  method = "CBS",
  minSeg = 100,
  smooth = 3,
  collapse.amb = TRUE
)

Arguments

parent1	A path to a VCF file to be loaded for a parent 1.
parent2	A path to a VCF file to be loaded for a parent 2.
child	A path to a VCF file to be loaded for a child.
genome	A reference genome used by readVcfAsVRanges function. [e.g. 'hg38' - human]
method	A user defined method to be used to map changes in haplotype blocks [default: CBS]
minSeg	Minimal length (number of variants) being reported as haplotype block (fastseg parameter).
smooth	Number of consecutive variants being considered as a random error and so being corrected (flipped).
collapse.amb	Set to TRUE if segments with ambiguous haplotype assignments should be collapsed.

Value

A list object that contains mapped meiotic breakpoints and inherited hapltype segments for each homolog in a child.

Author(s)

David Porubsky

daewoooo/StrandPhaseR documentation built on April 7, 2024, 7:13 p.m.