rle_ddrc: run length encoding to create segment files from DDRC.df

In SingerLab/gac: Genetic Analysis of Cells

run length encoding to create segment files from DDRC.df

Description

Still in development: currently performs RLE by chromosome and returns chromsome specific encoding. Locantions are not currently offsest by chromsome start locations

Usage

rle_ddrc(cnr, chrom = "bin.chrom", pos = "bin.start")

Arguments

cnr	a cnr bundle
chrom	name of column in chromInfo to use as chromosomes
pos	name of column in chromInfo to use as chromosomal position

Value

A run length encoding table from the clone profiles contained in DDRC.df

Examples

data(cnr)

noisy.cells <- cnr$qc$cellID[cnr$qc$qc.status == "FAIL"]

## reduced pipeline to genrate DDRC clone profiles
cnr <- excludeCells(cnr, excl = noisy.cells)
cnr <- phylo_cnr(cnr, root.cell = "cell0")
cnr <- setBrayClusters(cnr)
cnr <- run_consensus_clustering(cnr, iters = 20, maxK = 40)
cnr <- doKSpectral(cnr)
cnr <- setKcc(cnr)
cnr <- cluster_heterogeneity(cnr, by = "category1",
          cluster_column = "ConsensusC")
cnr <- get_cluster_profiles(cnr)

ddrc_rle <- rle_ddrc(cnr)

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