Description Usage Arguments Details Value Author(s) References Examples

Clusters cells according to their copy number profile.

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`cnps` |
Segment-by-cell matrix of copy number states (output of |

`k` |
Desired number of clusters (see also |

`h` |
Threshold used to define clones from hierarchical clustering result. A subtree is defined as a clone if the maximum distance between its cell members is less than 100* |

`weights` |
Vector of weights assigning differential importance to segments (typically calculated based on segment lengths). |

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

`chrOrder` |
Specifies order in which chromosomes should be plotted. |

`HFUN` |
Agglomeration method used to compute the hierarchical clustering (see also |

`...` |
additional arguments passed on to |

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 *j* at locus *i*.
Pairwise distances between cells are calculated in Hamming space of their segmental copy number profiles (rows in CNF), weighted by segment length. Hierarchical clustering is used to build a tree of the cells from the distance matrix. 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.

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. |

Noemi Andor

Andor, N.*, Lau, B.*, Catalanotti, C., Kumar, V., Sathe, A., Belhocine, K., Wheeler, T., et al. (2018) Joint single cell DNA-Seq and RNA-Seq of gastric cancer reveals subclonal signatures of genomic instability and gene expression. doi: https://doi.org/10.1101/445932

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noemiandor/liayson documentation built on Dec. 13, 2018, 10:24 p.m.

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