TranscriptRanges: Transcript ranges data
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')
Description
Usage
Format
Details
Source
Examples
Description
Transcript ranges and strand information for a particular reference genome.
Usage
1
2
3
4
5
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
1
2
3
4
5
6
7
8
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 April 3, 2021, 5:07 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Format Details Source Examples
Description
Transcript ranges and strand information for a particular reference genome.
Usage
1 2 3 4 5 |
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
1 2 3 4 5 6 7 8 | 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
# ... ... ... ... ... ...
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.