expands (version 1.7.2)

buildMultiSamplePhylo: Relations between inter- and intra-sample subpopulations

Description

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.

Usage

buildMultiSamplePhylo(samGr,out,treeAlgorithm="bionjs",ambigSg=F,plotF=1,spRes=1)

Arguments

samGr

List with three fields: cbs - 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). sps - Output of runExPANdS. Matrix in which each row corresponds to a somatic mutations. 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 asssigned; PM - the total ploidy of all alleles at the mutated genomic locus, in the assigned subpopulation; PM_B - the ploidy of the B-allele at the mutated genomic locus, in the assigned subpopulation; CN_Estimate - the average ploidy (among all cells) of the locus in which the mutation is embedded (see also assignQuantityToMutation). label - 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.

ambigSg

Input parameter "keepAmbigSeg" for called function: assignQuantityToSP.

plotF

Option for displaying a visual representation of the phylogenetic tree (0 - no display; 1 - display). Default: 1.

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).

Value

Details

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 ploidy and point mutations information are excluded from phylogeny.

See Also

buildPhylo