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

strandPhaseR

R Documentation

Wrapper function

Description

This function will move through .bam files in a folder and perform several steps (see Details).

Usage

strandPhaseR(
  inputfolder,
  outputfolder = "./StrandPhaseR_analysis",
  configfile = NULL,
  numCPU = 1,
  positions = NULL,
  WCregions = NULL,
  chromosomes = NULL,
  pairedEndReads = TRUE,
  min.mapq = 10,
  min.baseq = 20,
  num.iterations = 2,
  translateBases = TRUE,
  concordance = 0.9,
  fillMissAllele = NULL,
  splitPhasedReads = FALSE,
  compareSingleCells = FALSE,
  exportVCF = NULL,
  bsGenome = NULL,
  ref.fasta = NULL,
  assume.biallelic = FALSE
)

Arguments

`inputfolder`	Path to the bam files to process
`outputfolder`	Output directory. If non-existent it will be created.
`numCPU`	The numbers of CPUs that are used. Should not be more than available on your machine.
`positions`	Filename with listed position of SNVs for given chromosome (format: chrName SNVpos).
`WCregions`	Filename of all WC region for a given chromosome (format: chrName:Start:End:FileName).
`pairedEndReads`	Set to `TRUE` if you have paired-end reads in your file.
`min.mapq`	Minimum mapping quality when importing from BAM files.
`min.baseq`	Minimum base quality to consider a base for phasing.
`num.iterations`	Number of iteration to sort watson and crick matrices.
`translateBases`	translates integer coded bases (1,2,3,4) into letters (A,C,G,T)
`concordance`	Level of agreement between single cell and consensus haplotypes
`fillMissAllele`	A patch to a single BAM or VCF file for a given sample to be used to fill missing alleles, uncovered in Strand-seq data.
`splitPhasedReads`	Set to `TRUE` if you want to split reads per haplotype.
`compareSingleCells`	Set to `TRUE` if you want to compare haplotypes at the single-cell level.
`exportVCF`	Ideally a sample ID that if defined invokes export of phased haplotypes in a separate VCF file.
`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.