saveClusteredCells: Saving clones to user-defined output.

In 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, expression, ccMembership, sName, outD)

Arguments

outc	Output of clusterCells or assignCellsToClusters: list containing segment-by-cell matrix, clone membership of each cell and the underlying dendrogram.
expression	Gene-by-cell matrix of expression.
ccMembership	List with each entry containing all cell IDs associated with a given cell cycle state. Must include entry 'G1Malignant', containing the IDs of G0G1 tumor cells.
sName	Prefix for the output files (typically the sample name).
outD	The output directory.

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). 5. For each clone, a segment-by-cell matrix of copy number states for all cell members of that clone.

Author(s)

Noemi Andor

liayson documentation built on Sept. 30, 2022, 1:07 a.m.