saveClusteredCells: Saving clones to user-defined output.

In noemiandor/liayson: Linking Singe-Cell Transcriptomes Atween Contemporary Subpopulation Genomes

Saving clones to user-defined output.

Description

Writes clone statistics, dendrogram and clone-specific mutation profiles.

Usage

saveClusteredCells(outc, outD, sName)

Arguments

outc	Output of clusterCells or assignCellsToClusters: list containing segment-by-cell matrix, clone membership of each cell and the underlying dendrogram.
outD	The output directory.
sName	Prefix for the output files (typically the sample name).

Details

Writes each of the following aspects of a sample's clonal composition into an output file:
1. The clone membership of each cell (*.spstats)
2. The segment-by-cell matrix of copy number states (*.sc.cbs)
3. The consensus copy number profile of each detected clone, calculated as the average profile of cells that are members of the respective clone (*.sps.cbs)
4. The cell dendrogram (*.tree).

Author(s)

Noemi Andor

noemiandor/liayson documentation built on March 31, 2022, 7:39 a.m.