gatherEXPANDSoutput: Reading EXPANDS' output files

In expands: Expanding Ploidy and Allele-Frequency on Nested Subpopulations

Description

Reads EXPANDS output files from user-specified input directory.

Usage

gatherEXPANDSoutput(outDirEXPANDS,regex="")

Arguments

outDirEXPANDS	Absolute path to input directory in which EXPANDS results are stored, as generated by runExPANdS.
regex	Pattern that path has to match in order to be read.

Value

Two-level nested list. The outer level contains one entry per each output of runExPANdS. Each entry constitutes an inner list with fields:
snv - The assignment of each SNV to a subpopulation.
cbs - The copy number of each genomic segment in each subpopulation.
spstats - Matrix of predicted subpopulations.
tree - The inferred phylogenetic relationships between subpopulations as an object of class "phylo4" (library phylobase).
treeApe - The inferred phylogenetic relationships between subpopulations as an object of class "phylo" (library ape).

Author(s)

Noemi Andor

See Also

runExPANdS

expands documentation built on Sept. 5, 2021, 5:18 p.m.