A conveniece wrapper function for hmmcopy_singlecell() to test multiple candidate multiplier (aka ploidy) values and return either the best result, or a list of all results for downstream analysis.
Usage
run_sc_hmmcopy(
chr,
start,
end,
counts,
reads,
ideal = rep(TRUE, length(counts)),
param = params_sc_hmm(),
cell_id,
multipliers = 1:6,
verbose = FALSE,
maxiter = 200,
n_cutoff = NULL,
return = c("best", "all")
)Arguments
- chr
Vector of chromosomes
- start
Vector of bin start positions
- end
Vector of bin end positions
- counts
Vector of bin corrected counts. These should ideally be GC corrected counts from
gc_cor_modal()- reads
A vector of raw read counts per bin
- ideal
A logical vector indicating which bins are ideal for analysis. See
is_ideal_bin()- param
A matrix of parameter values in columns for each state in rows. See
HMMcopy::HMMsegment()for more information.- cell_id
Cell id
- multipliers
Positive integer list of ploidy multipliers to test
- verbose
Print verbose
- maxiter
The maximum number of iterations allows for the Maximum-Expectation algorithm, reduce to decrease running time at the expense of robustness.
- n_cutoff
Cutoff for the number of bins in a given state for calculating the
true_multipliervalue. Defaults to 5% of bins.- return
a character. One of
bestorallto either return the result for the best ploidy only, or a list of results for all ploidies