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

View source: R/convert_seg_to_bins.R

rle_ddrcR Documentation

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 <- phyloCNR(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 Oct. 14, 2022, 4:09 a.m.