correctInvertedRegionPhasing: Correct StrandPhaseR phasing over inverted regions
In daewoooo/StrandPhaseR: Phase template strands from Strand-seq data

View source: R/correctInversionPhasing.R

correctInvertedRegionPhasing

R Documentation

Correct StrandPhaseR phasing over inverted regions

Description

This function attempts to correct phasing over inverted regions using both breakpointR and StrandPhaseR results.

Usage

correctInvertedRegionPhasing(
  input.bams,
  outputfolder = NULL,
  inv.bed = NULL,
  recall.phased = FALSE,
  het.genotype = "strict",
  chromosomes = NULL,
  snv.positions = NULL,
  composite.file = NULL,
  breakpointR.data = NULL,
  strandphaseR.data = NULL,
  pairedEndReads = TRUE,
  min.mapq = 10,
  background = 0.05,
  vcfs.files = NULL,
  lookup.bp = 1e+06,
  lookup.blacklist = NULL,
  bsGenome = NULL,
  ref.fasta = NULL,
  assume.biallelic = TRUE,
  overwrite.results = TRUE
)

Arguments

`input.bams`	A path to a VCF file to be loaded.
`outputfolder`	A path to a folder where all summary and intermediate results will be stored.
`inv.bed`	A BED formatted file that contains likely inverted regions to evaluate.
`recall.phased`	If set to `TRUE`,inversion signatures will be re-called using phased Strand-seq reads (Useful to redefine HET inversion boundaries).
`het.genotype`	If set to 'strict' heterozygous inversion has to be supported by both 'breakpointR.data' and 'strandphaseR.data', if set to 'lenient' support from either 'breakpointR.data' only is sufficient.
`chromosomes`	Limit analysis to a certain chromosomes only.
`snv.positions`	A path to a VCF files containing SNV positions to phase.
`composite.file`	...
`breakpointR.data`	A path to results obtained by running `breakpointR` package on a given sample.
`strandphaseR.data`	A path to results obtained by running `StrandPhaseR` package on a given sample.
`pairedEndReads`	Set to `TRUE` if you have paired-end reads in your file.
`min.mapq`	Minimum mapping quality when importing from BAM files.
`vcfs.files`	A path to a folder where all VCF files to be corrected are stored (sample specific).
`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.
`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.
`overwrite.results`	Set to `FALSE` if existing corrected VCF files should be used instead of creating a new copy of original VCF file.