sigminer (version 0.1.11)

get_matrix: Generate a sample-by-component matrix

Description

Generate a sample-by-component matrix representing the sum of posterior probabilities of each copy-number event being assigned to each component.

Usage

get_matrix(CN_features, all_components = NULL, cores = 1,
  rowIter = 1000)

Arguments

CN_features

a list contains six copy number feature distributions, obtain this from get_features() function.

all_components

a list contain flexmix object of copy-number features, obtain this from get_components function or use pre-compiled components data which come from CNV signature paper https://www.nature.com/articles/s41588-018-0179-8 (set this parameter as NULL).

cores

number of compute cores to run this task. You can use parallel::detectCores() function to check how many cores you can use.

rowIter

step size of iteration for rows of ech CNV feature.

Value

a numeric sample-by-component matrix

See Also

Other internal calculation function series: get_ArmLocation, get_LengthFraction, get_cnlist, get_cnsummary_sample, get_components, get_features

Examples

# NOT RUN {
# Load copy number components
load(system.file("extdata", "toy_cn_components.RData",
  package = "sigminer", mustWork = TRUE
))
# Load copy number features
load(system.file("extdata", "toy_cn_features.RData",
  package = "sigminer", mustWork = TRUE
))

cn_matrix <- get_matrix(cn_features, cn_components)
# }