annotate.non25M.genomic.transcrits_wise: Map non-25M genomic mapppings to transcripts coordinates

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

Description

Map genomic alignment coordinated to transcript coordinates

Usage

annotate.non25M.genomic.transcrits_wise(Alignment.genomic.non25M, Annotation)

Arguments

Alignment.genomic.non25M	data.frame of raw genomic alignment, subsetted to non-25M mappings (CIGAR != "25M")
Annotation	data.frame, reference genome annotation, must contatin feature column, and feature names must contain "transcript" or "RNA"

Details

Mappings in the genomic alignment data.frame are devided into two parts: those that have CIGAR == "25M" and those that have CIGAR != "25M". The first ones are mapped to exon coordinated from the Reference Annotation, and the second ones are suspects to be exon-exon border mappings, which is why they are mapped to transcript coordinates.

Value

returns a data.frame

Author(s)

Vladislava Milchevskaya [e-mail]

See Also

annotate.G.alignment

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