TranscriptRanges: Transcript ranges data
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

TranscriptRanges

R Documentation

Transcript ranges data

Description

Transcript ranges and strand information for a particular reference genome.

Usage

trans.ranges.GRCh37

trans.ranges.GRCh38

trans.ranges.GRCm38

Format

A data.table which contains transcript range and strand information for a particular reference genome. colnames are chrom, start, end, strand, Ensembl.gene.ID, gene.symbol. It uses one-based coordinates.

An object of class data.table (inherits from data.frame) with 19083 rows and 6 columns.

An object of class data.table (inherits from data.frame) with 19096 rows and 6 columns.

An object of class data.table (inherits from data.frame) with 20325 rows and 6 columns.

Details

This information is needed to generate catalogs that depend on transcriptional strand information, for example catalogs of class SBS192Catalog.

trans.ranges.GRCh37: Human GRCh37.

trans.ranges.GRCh38: Human GRCh38.

trans.ranges.GRCm38: Mouse GRCm38.

For these two tables, only genes that are associated with a CCDS ID are kept for transcriptional strand bias analysis.

This information is needed for StrelkaSBSVCFFilesToCatalog,
StrelkaSBSVCFFilesToCatalogAndPlotToPdf, MutectVCFFilesToCatalog,
MutectVCFFilesToCatalogAndPlotToPdf, VCFsToSBSCatalogs and VCFsToDBSCatalogs.

Source

ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/GRCh37_mapping/gencode.v30lift37.annotation.gff3.gz

ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gff3.gz

ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M21/gencode.vM21.annotation.gff3.gz

Examples

trans.ranges.GRCh37
# chrom    start      end strand Ensembl.gene.ID  gene.symbol
#     1    65419    71585      + ENSG00000186092        OR4F5
#     1   367640   368634      + ENSG00000235249       OR4F29
#     1   621059   622053      - ENSG00000284662       OR4F16
#     1   859308   879961      + ENSG00000187634       SAMD11
#     1   879583   894689      - ENSG00000188976        NOC2L
#   ...      ...      ...    ...             ...          ...

ICAMS documentation built on June 15, 2025, 1:08 a.m.