getTransChromFusions: Detect trans-chromosomal mappings of Iso-seq reads

View source: R/getTransChromFusions.R

getTransChromFusionsR Documentation

Detect trans-chromosomal mappings of Iso-seq reads

Description

This function reads BAM file into a GRanges object and searches for reads that map do different chromosomal locations. Links supported by user defined number of reads are reported and points to a putative gene fusions.

Usage

getTransChromFusions(
  bamfile = NULL,
  min.mapq = 10,
  standardChroms = TRUE,
  min.links = 5
)

Arguments

bamfile

Bamfile with aligned reads.

min.mapq

Minimum mapping quality when importing from BAM files.

standardChroms

If set to TRUE only standard chromosomes (1-22, X & Y) will be kept.

min.links

Minimum number of supporting Iso-seq reads in order to report a putative gene fusion.

Value

A GRanges object reporting all found links.

Author(s)

David Porubsky


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