phaseHETinversion: Phase a heterozygous inversion using Strand-seq data
In daewoooo/StrandPhaseR: Phase template strands from Strand-seq data

View source: R/correctInversionPhasing.R

phaseHETinversion

R Documentation

Phase a heterozygous inversion using Strand-seq data

Description

This function takes as an input region deemed to be a heterozygous inversion and attempts to phase SNVs inside this region using haplotype informative Strand-seq reads from multiple single cells.

Usage

phaseHETinversion(
  input.bams = NULL,
  snv.positions = NULL,
  phase.gr = NULL,
  lookup.bp = 1e+06,
  lookup.blacklist = NULL,
  pairedEndReads = TRUE,
  min.mapq = 10,
  bsGenome = NULL,
  ref.fasta = NULL,
  assume.biallelic = TRUE,
  verbose = FALSE
)

Arguments

`input.bams`	A path to a VCF file to be loaded.
`snv.positions`	A path to a VCF files containing SNV positions to phase.
`phase.gr`	A `GRanges` object containing a single region to be phased. This region should point to a heterozygous inversion site.
`lookup.bp`	A number of nucleotides, downstream and upstream, from the heterozygous inversion site ('phase.gr') to be genotyped.
`lookup.blacklist`	A `GRanges` object or a path to a BED file containing a set of ranges to be excluded when extending 'phase.gr' by 'lookup.bp'. The total size of 'lookup.bp' is kept after filtering.
`pairedEndReads`	Set to `TRUE` if you have paired-end reads in your file.
`min.mapq`	Minimum mapping quality when importing from BAM files.
`bsGenome`	A `BSgenome` object which contains reference genome used to infer reference alleles.
`ref.fasta`	A user defined reference FASTA file to extract reference allele for all SNV positions.
`assume.biallelic`	If set to `TRUE` parameter 'snv.positions' is expected to contain biallelic loci (0/1, 1/0) and thus gaps in haplotypes will be filled accordingly.
`verbose`	Is set to `TRUE` function will provide a more detailed messaging of ongoing analysis steps.