chromInfo: Chromosome coordinates and additional data of the bins

In SingerLab/gac: Genetic Analysis of Cells

Chromosome coordinates and additional data of the bins

Description

A data.frame containing the chromsome and end coordiantes for all the bins of the single-cell copy number matrix 'copynumbers'. This table is used for SCclust, some data may be recurrent now to preserve compatibility with that package and the functions here. This table is cross referenced to create the 'genes' table, an interpolated table to link the bins to genes

Usage

data(chromInfo)

Format

A data frame with chromosome and position information

• bin.chrom, object class 'factor' corresponding to the chromosome of the bin.

• bin.start, starting coordinate of the bin

• bin.start.abspos, cumulative start positions of the bins

• bin.end, end coordinate of the bin

• bin.length, size of the bin

• mappable.positions, number of mappable positions

• gc.content, percent gc content

• chrom.numeric, a numeric representation of the autosomes (e.g. 1..24 for hg19, 1..23 for mm10, 1..30 for bta9

• chrom, alternate representation of the chromosome to bind to X for SCclust

• chrompos, alternate representation of the bin.start to bind to X for SCclust

• abspos, alternate representation of the chromosome to bind to X for SCclust

Source

https://github.com/SingerLab/gac

SingerLab/gac documentation built on March 23, 2024, 5:15 a.m.