expand2genes: Expands the bins to genes

In SingerLab/gac: Genetic Analysis of Cells

Expands the bins to genes

Description

This function interpolates the bins into an interpretable gene copy number matrix. All genes within the bin coordinates get assigned the same value. Some genes sit between bins without copy number data and will be marked as NA

Usage

expand2genes(X, gene.index, bin.id = "bin.id", gene.id = "hgnc.symbol")

Arguments

X	the X bins data.frame
gene.index	gene index with bin.id and hgnc.symbol
bin.id	name of the bin.id column (the bin.id is the row in the bins data.frame)
gene.id	string noting which gene ID you want to use e.g. hgnc.symbol, ensembl_gene_id

Details

The gene copy number matrix is core to the cnr object.

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