buildMultiSamplePhylo: Relations between inter- and intra-sample subpopulations
In expands: Expanding Ploidy and Allele-Frequency on Nested Subpopulations

Description Usage Arguments Details Value Author(s) See Also

Predicts phylogenetic relations between subpopulations from subpopulation specific copy number and point mutation profiles, while including information about sample origin of each subpopulation. This function differs from buildPhylo in that it integrates the subpoulations predicted in multiple, geographically distinct tumor-samples into one common phylogeny and in that it includes point mutations in addition to copy number variations to infer inter-sample phylogenetic relations.

1	buildMultiSamplePhylo(samGr, out, treeAlgorithm="bionjs", e=0, plotF=1, spRes=1, v=F)

`samGr`	List with three fields: cbs - Input of `runExPANdS`: matrix in which each row corresponds to a copy number segment. CBS is typically the output of a circular binary segmentation algorithm. Columns in CBS must be labeled and must include chr, startpos, endpos and CN_Estimate (see `cbs`). Do not use the output of `runExPANdS` here. sps - Output of `runExPANdS`. Matrix in which each row corresponds to a somatic mutation. Columns must include: chr - the chromosome on which each mutation is located; startpos - the genomic position of each mutation; SP - the subpopulation to which the mutation has been assigned; PM - the total count of all alleles at the mutated genomic locus, in the assigned subpopulation; PM_B - the count of the B-allele at the mutated genomic locus, in the assigned subpopulation; CN_Estimate - the average copy number (among all cells) of the locus in which the mutation is embedded (see also `assignQuantityToMutation`). labels - Label denoting sample origin of each subpopulation matrix. Entry is mandatory for each geographical sample.
`out`	Prefix of file to which multi-sample phylogeny will be saved.
`treeAlgorithm`	Neighbor joining algorithm used for phylogeny reconstruction (from library ape). Options: bionjs (default), njs.
`e`	Input parameter "e" for called function: `assignQuantityToSP`.
`plotF`	Option for displaying the phylogenetic tree (0 - no display; 1 - display).
`spRes`	Option on whether or not to ignore the subpopulations calculated for each sample and instead treat every geographical tumor-sample as one single tumor-metapopulation (Default value: 1 - subpopulation resolution; 0 - metapopulation resolution).
`v`	Give a more verbose output.

This function does not change the subpopulation membership of SNVs. Instead it reconstructs phylogenetic relationships between subpopulations using neighbor-joining algorithms provided by R-package 'ape'. Pairwise distances between subpopulations i and j are calculated as:
d_{ij}:=(cnv_{i=j} + snv_{i=j})/(cnv_{ij}+snv_{ij}), where cnv_{i=j} is the number of copy number segments for which subpopulations i and j have the same copy number; snv_{i=j} is the number of point mutations for which subpopulations i and j have the same mutation status and cnv_{ij}, snv_{ij} are the total number of copy number segments and mutations respectively, for which both subpopulations have available information. Subpopulations with insufficient copy number and point mutations information are excluded from phylogeny.