txUnique: Count number of bases unique to each transcript

Description Usage Arguments Details Value Author(s)

View source: R/txUnique.R

Description

For each transcript, number of unique bases and total number of bases will be reported.

Usage

1
txUnique(GTF_Annotation_File, Feature_Type = "exon", Gene_ID_Attribute = "gene_id", Transcript_ID_Attribute = "transcript_id")

Arguments

GTF_Annotation_File

character string giving the name of a GTF file containing the transcript-level annotations.

Feature_Type

character string specifying the type of annotations. Only the annotations of the given type will be loaded from the GTF file. exon by default. The third column in the GTF file contains the type of the annotation in each line

Gene_ID_Attribute

character string specifying the attribute name in the 9-th column in the GTF file for the gene identifier. gene_id by default.

Transcript_ID_Attribute

character string specifying the attribute name in the 9-th column in the GTF file for the transcript identifier. transcript_id by default.

Details

This function compares the transcripts belonging to the same gene and then counts the number of bases unique to each transcript. It also reports the total number of bases for each transcript. When a transcript is found to contain overlapping exons, the overlapping exons will be merged and each overlapping base will be counted only once.

Value

A data matrix in which each row represents a transcript. The matrix includes four columns: gene identifier, transcript identifier, number of bases unique to each transcript and total number of bases each transcript has.

Author(s)

Yang Liao and Wei Shi


Bioconductor-mirror/Rsubread documentation built on July 14, 2017, 8:49 a.m.