getExonExonBorder: What function does (short)

In VladaMilch/pdProbeRemap: What the package does (short line)

Description

finds exon-exon border probes and corresponding transcripts

Usage

getExonExonBorder(Als, Annotation, level)

Arguments

Als	object of the class Alignment
Annotation	data.frame, reference genome annotation
level	character string, equals "gene" or "transcript"

Details

Identifies which probes fall into a transcript region in the reference genome annotation, and map simultaneously to the left end of one exon and to the left end of another exon of the same transcript, based on their CIGAR string and coordinates in the raw genomic alignment. Only mapping that have CIGAR != "25M" are considered.

Value

a "output type".

Author(s)

Vladislava Milchevskaya [e-mail]

See Also

function or class name

VladaMilch/pdProbeRemap documentation built on May 28, 2019, 3:21 p.m.