loadMatrices: This funcion will read in partial single cell haplotypes into...

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

This funcion will read in partial single cell haplotypes into two parallel matrices separately for Watson and Crick reads

Description

This funcion will read in partial single cell haplotypes into two parallel matrices separately for Watson and Crick reads

Usage

loadMatrices(
  inputfolder = NULL,
  positions = NULL,
  WCregions = NULL,
  pairedEndReads = FALSE,
  min.mapq = 10,
  min.baseq = 30
)

Arguments

inputfolder	Path to the bam files to process
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.

Author(s)

David Porubsky

daewoooo/StrandPhaseR documentation built on Jan. 17, 2025, 7:44 a.m.