genotypeRegions: Calculate genotype in a set of genomic ranges

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

Calculate genotype in a set of genomic ranges

Description

This function exports genotype information for a set of user defined genomic ranges.

Usage

genotypeRegions(
  regions = NULL,
  directional.reads = NULL,
  blacklist = NULL,
  min.reads = 5,
  alpha = 0.05,
  index = NULL
)

Arguments

regions	A GRanges-class object that contains genomic regions to be genotyped.
directional.reads	A GRanges-class object that contains directional Strand-seq reads.
blacklist	A GRanges-class object containing regions to be excluded from genotyping.
min.reads	Minimal number of reads to pursue genotyping.
alpha	Estimated level of background in Strand-seq reads.
index	User defined character string to be appended to calculated genotypes.

Value

A GRanges-class object with appended count of plus and minus reads and the most likely genoptype.

Author(s)

David Porubsky

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