ICAMS (version 2.0.7)

TranscriptRanges: Transcript ranges data

Description

Transcript ranges and strand information for a particular reference genome.

Usage

trans.ranges.GRCh37

trans.ranges.GRCh38

trans.ranges.GRCm38

Arguments

Format

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

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.

Examples

Run this code
# NOT RUN {
trans.ranges.GRCh37
# chrom    start      end strand gene.name
#     1    65419    71585      +     OR4F5
#     1   367640   368634      +    OR4F29
#     1   621059   622053      -    OR4F16
#     1   859308   879961      +    SAMD11
#     1   879583   894689      -     NOC2L
#   ...      ...      ...    ...       ...

# }

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