View source: R/convert_seg_to_bins.R
rle_ddrc | R Documentation |
Still in development: currently performs RLE by chromosome and returns chromsome specific encoding. Locantions are not currently offsest by chromsome start locations
rle_ddrc(cnr, chrom = "bin.chrom", pos = "bin.start")
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 |
A run length encoding table from the clone profiles contained in DDRC.df
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)
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