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: |
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: |
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.
An object of class "phylo" (library ape).
Noemi Andor
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