writeStandardFinalOutput: Function that stores the final output in a unified format on...

In Wedge-Oxford/dpclust: DPClust - An R package for subclonal reconstruction of tumours using sequencing data

Function that stores the final output in a unified format on disk

Description

Function that stores the final output in a unified format on disk

Usage

writeStandardFinalOutput(clustering, dataset, most.similar.mut,
  outfiles.prefix, outdir, samplename, subsamplenames, GS.data, density,
  polygon.data, no.iters, no.iters.burn.in, min_muts_cluster,
  min_frac_muts_cluster, assign_sampled_muts = T, write_tree = F,
  generate_cluster_ordering = F, no.samples.cluster.order = 1000)

Arguments

clustering	A clustering result
dataset	The dataset that went into clustering
most.similar.mut	Vector containing for each non-sampled mutation its most similar sampled mutation. The non-sampled mutation will be assigned to the same cluster
outfiles.prefix	A prefix for the filenames
outdir	Output directory where the replot of the 1D method is to be stored if clusters are removed due to being too small
samplename	Overall samplename
subsamplenames	Samplenames of the different timepoints
GS.data	MCMC output
density	Posterior density estimate across MCMC iterations
polygon.data	1D confidence interval, used for plotting the 1D method (set to NA for multi-D method)
no.iters	Number of total iterations
no.iters.burn.in	Number of iterations to be used as burn-in
min_muts_cluster	The minimum number of mutations required for a cluster to be kept in the final output
min_frac_muts_cluster	The minimum fraction of mutations required for a cluster to be kept in the final
assign_sampled_muts	Boolean whether to assign the non-sampled mutations (Default: TRUE)
write_tree	Boolean whether to write a tree to file. Not all clustering methods return a tree (Default: FALSE)
generate_cluster_ordering	Boolean specifying whether a possible cluster ordering should be determined (Default: FALSE)
no.samples.cluster.order	Number of mutations to sample (with replacement) to classify pairs of clusters into parent-offspring or siblings (Default: 1000)

Author(s)

sd11

Wedge-Oxford/dpclust documentation built on July 6, 2024, 2:02 p.m.