create_annotation: Annotation data table.

In LabTranslationalArchitectomics/riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

Annotation data table.

Description

This function generates transcript basic annotation data tables starting from GTF files or TxDb objects. Annotation data tables include a column named transcript reporting the name of the reference transcripts and four columns named l_tr, l_utr5, l_cds and l_utr3 reporting the length of the transcripts and of their annotated 5' UTRs, CDSs and 3' UTRs, respectively. Please note: if a transcript region is not annotated its length is set to 0.

Usage

create_annotation(gtfpath = NULL, txdb = NULL, dataSource = NA, organism = NA)

Arguments

gtfpath	A character string specifying the path to a GTF file, including its name and extension. Please make sure the GTF file derives from the same release of the sequences used in the alignment step. Note that either gtfpath or txdb must be specified. Default is NULL.
txdb	Character string specifying the TxDb annotation package to be loaded. If not already present in the system, it is automatically installed through the biocLite.R script (check here the list of available TxDb annotation packages). Please make sure the TxDb annotation package derives from the same release of the sequences used in the alignment step. Note that either gtfpath or txdb must be specified. Default is NULL.
dataSource	Optional character string describing the origin of the GTF data file. This parameter is considered only if gtfpath is specified. For more information about this parameter please refer to the description of dataSource of the makeTxDbFromGFF function included in the GenomicFeatures package.
organism	Optional character string reporting the genus and species of the organism of the GTF data file. This parameter is considered only if gtfpath is specified. For more information about this parameter please refer to the description of organism of the makeTxDbFromGFF function included in the GenomicFeatures package.

Value

A data table.

Examples

## gtf_file <- "path/to/GTF/file.GTF"
## create_annotation(gtfpath = gtf_file, dataSource = "gencode6", organism = "Mus musculus")

LabTranslationalArchitectomics/riboWaltz documentation built on Jan. 17, 2024, 12:18 p.m.