| TranscriptRanges {ICAMS} | 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/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
# ... ... ... ... ... ...