HoneyBADGER_calcGexpCnvBoundaries: Recursive HMM to identify CNV boundaries using normalized...

In JEFworks/HoneyBADGER: HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data

Description

Recursive HMM to identify CNV boundaries using normalized gene expression data

Arguments

gexp.norm.sub	Optional normalized gene expression matrix. Useful for manual testing of restricted regions. If NULL, gexp.norm within the HoneyBADGER object will be used.
chrs	List of chromosome names. Genes not mapping to these chromosomes will be excluded. Default autosomes only: paste0('chr', c(1:22))
min.traverse	Depth traversal to look for subclonal CNVs. Higher depth, potentially smaller subclones detectable. (default: 3)
min.num.genes	Minimum number of genes within a CNV. (default: 5)
t	HMM transition parameter. Higher number, more transitions. (default: 1e-6)
init	Initialize recursion (default: FALSE)
verbose	Verbosity (default: FALSE)
...	Additional parameters for calcGexpCnvProb

JEFworks/HoneyBADGER documentation built on July 24, 2021, 3:01 p.m.