clusterCells: Grouping cells into clones.

Description Usage Arguments Details Value Examples

View source: R/clusterCells.R

Description

Clusters cells according to their copy number profile.

Usage

1
2
clusterCells(cnps, k=NA, h=NA, consolidate=1, weights=NULL, minSegLength=1E6, 
   colCol=NULL, rowCol=NULL, main="", chrOrder=NULL, cexRow = 0.07, trace ="none")

Arguments

cnps

Segment-by-cell matrix of copy number states (output of segmentExpression2CopyNumber).

consolidate

Whether or not to homogenize the profiles of cells with same clone membership (consolidate=0 <=> all cells within a clone will be identical; consolidate=1 <=> intra-clone homogeneity not enforced).

minSegLength

Minimum number of base pairs below which a segment is to be excluded when defining clones.

Details

Let CNF be the matrix of copy number states per non-private segment per cell, with entries (i, j) pointing to the copy number state of cell i at locus j. Pairwise distances between cells are calculated in Euclidean space of their segmental copy number profiles (rows in CNF), weighted by segment length. Hierarchical clustering with the ward.D2 agglomeration method is used to build a phylogenetic tree of the cells. A subtree is defined as a clone if the maximum distance between its cell members is less than a user-defined fraction of the genome (h.
Alternatively, if k is set, the tree is cut to obtain k clones.
If neither h nor k are set, Akaike information criterion is used to decide on anywhere between 1 and 30 clones.

Value

List with three fields:

cnps

Segment-by-cell matrix of copy number states.

sps

The clone membership of each cell (that is, columns in cnps).

tree

An object of class hclust which describes the tree produced by the clustering process.

Examples

1
2
data(cnps)
outc = clusterCells(cnps, h=0.15)

noemiandor/liayson documentation built on Oct. 27, 2018, 12:15 a.m.