gene.index: Bin-to-gene index

In SingerLab/gac: Genetic Analysis of Cells

Bin-to-gene index

Description

This table was constructed by mapping bin regions to gene coordinates. We found the simplest way to do this, was to pull the gencode annotation with biomaRt[https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html] and use findOverlap with GenomicRanges[https://bioconductor.org/packages/release/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.html]. The resulting GRanges object was saved as a text file.

Usage

data(gene.index)

Format

A data frame with chromosome and position information

• chrom, chromosome

• start, gene start coordinate

• end, gene end coordinate

• width, width

• strand, gene strand

• ensembl_gene_id, ENSEMBL gene ID

• hgnc.symbol, HGNC gene symbol

• gene.type, gene type

• bin.id, bin ID

#' @docType data

Details

A table to interpolate bin copy number to individual genes.

Source

https://github.com/SingerLab/gac

SingerLab/gac documentation built on March 16, 2023, 2:52 p.m.