synchronizeReadDirRegion: Synchronize Strand-seq read directionality

In daewoooo/primatR: What the Package Does (TODO)

Synchronize Strand-seq read directionality

Description

This function aims to synchronize read directionality of a specified genomic region.

Usage

synchronizeReadDirRegion(
  bamfiles = "",
  region = NULL,
  pairedEndReads = TRUE,
  min.mapq = 10,
  filterAltAlign = TRUE,
  alpha = 0.1,
  genot.frac.reads = 0.25,
  genot.region.ends = "right",
  desired.genot = c("cc", "ww")
)

Arguments

bamfiles	A list of BAM files to be processed.
region	A GRanges-class object to select reads from.
pairedEndReads	Set to TRUE if you have paired-end reads in your file.
min.mapq	Minimum mapping quality when importing from BAM files.
filterAltAlign	Set to TRUE if you want to filter out reads with alternative mapping location.
alpha	Estimated level of background in Strand-seq reads.
genot.frac.reads	A fraction of the total number of reads to be genotype from both or a single end of a given 'region' based on 'genot.region.ends'.
genot.region.ends	Define if 'left' or 'right' of 'both ends of a given region shall be genotyped.
desired.genot	Select desired genotypes: 'ww', 'cc', 'wc' to be allowed on selected region ends. If 'genot.region.ends' = 'both', both ends have to have the same genotype.

Value

A GRanges-class object that reads synchronized by directionality.

Author(s)

David Porubsky

daewoooo/primatR documentation built on Oct. 22, 2024, 9:41 p.m.