boot_fast_baps: boot_fast_baps

In gtonkinhill/fastbaps: A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model

boot_fast_baps

Description

Function to perform bootstrap replicated of fastbaps.

Usage

boot_fast_baps(
  sparse.data,
  k.init = NULL,
  n.replicates = 100,
  hc.method = "ward",
  n.cores = 1,
  quiet = TRUE
)

Arguments

sparse.data	a sparse SNP data object returned from import_fasta_sparse_nt
k.init	the initial number of clusters to start the bayesian hierarchical clustering from. Defaults to (number of sequences)/4
n.replicates	the number of bootstrap replicates to perform (default=100)
hc.method	the type of initial hierarchical clustering to use. Can be with 'ward' or 'genie' (default='ward')
n.cores	the number of cores to use in clustering
quiet	whether or not to print progress information (default=FALSE)

Value

a co-occurence count matrix

Examples

## Not run: 
fasta.file.name <- system.file("extdata", "seqs.fa", package = "fastbaps")
sparse.data <- import_fasta_sparse_nt(fasta.file.name)
boot.result <- boot_fast_baps(sparse.data)
dendro <- as.dendrogram(fast_baps(sparse.data))
heatmap(boot.result, dendro, dendro)

## End(Not run)

gtonkinhill/fastbaps documentation built on Sept. 25, 2022, 1:56 p.m.