cnv_models: Fit a series of Gaussian finite mixture models at a CNV...

In scristia/CNPBayes: Bayesian mixture models for copy number polymorphisms

Description

Fits a number of Gaussian finite mixture models at a CNV region for a collection of samples and returns a single best-fitting model.

Usage

cnv_models(mb, grange, snp_se, mp = McmcParams(iter = 1000, burnin = 200))

Arguments

mb	a MultiBatch instance
grange	GRanges object indicating the CNV region
snp_se	a SummarizedExperiment with assay data containing B allele frequencies at SNPs
mp	a McmcParams instance

Value

a MultiBatch instance

See Also

MultiBatch

Examples

path <- system.file("extdata", package="CNPBayes")
set.seed(555)
cnp_se <- readRDS(file.path(path, "cnp_se.rds"))["CNP_022", ]
snp_se <- readRDS(file.path(path, "snp_se.rds"))
snp_se <- subsetByOverlaps(snp_se, cnp_se)
path2 <- file.path(path, "CNP_022")
mb.subsamp <- readRDS(file.path(path2, "mb_subsamp.rds"))
## Not run: 
    mb <- cnv_models(mb.subsamp,
                     rowRanges(cnp_se)["CNP_022"],
                     snp_se)

## End(Not run)

scristia/CNPBayes documentation built on Aug. 9, 2020, 7:31 p.m.