readPairsAsLinks: Get significant connections between read pairs

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

Get significant connections between read pairs

Description

This function takes split read mappings of PacBio reads and keeps only genomic regions with at least 10 unique reads in a given (100kb) genomic bin.

Usage

readPairsAsLinks(
  inputfolder = ".",
  min.mapq = 60,
  filt.flag = 3328,
  min.reads = 10,
  chromosomes = NULL,
  bsgenome = NULL,
  blacklist = NULL
)

Arguments

inputfolder	A directory that contains set of BAM files to be processed.
min.mapq	Minimum mapping quality when importing from BAM files.
filt.flag	Filter out reads with a given flag.
min.reads	Minimum number of unique reads to support a link.
chromosomes	If only a subset of the chromosomes should be binned, specify them here.
bsgenome	A reference genome to get lengths of genomic sequences (eg. GRCh38).
blacklist	An GRanges-class object that contains regions to be filtered out.

Value

A ggplot object.

Author(s)

David Porubsky

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