Call CNVs in a pseudobulk profile using the Numbat joint HMM
Usage
analyze_bulk(
bulk,
t = 1e-05,
gamma = 20,
theta_min = 0.08,
logphi_min = 0.25,
nu = 1,
min_genes = 10,
exp_only = FALSE,
allele_only = FALSE,
bal_cnv = TRUE,
retest = TRUE,
find_diploid = TRUE,
diploid_chroms = NULL,
classify_allele = FALSE,
run_hmm = TRUE,
prior = NULL,
exclude_neu = TRUE,
phasing = TRUE,
verbose = TRUE
)Arguments
- bulk
dataframe Pesudobulk profile
- t
numeric Transition probability
- gamma
numeric Dispersion parameter for the Beta-Binomial allele model
- theta_min
numeric Minimum imbalance threshold
- logphi_min
numeric Minimum log expression deviation threshold
- nu
numeric Phase switch rate
- min_genes
integer Minimum number of genes to call an event
- exp_only
logical Whether to run expression-only HMM
- allele_only
logical Whether to run allele-only HMM
- bal_cnv
logical Whether to call balanced amplifications/deletions
- retest
logical Whether to retest CNVs after Viterbi decoding
- find_diploid
logical Whether to run diploid region identification routine
- diploid_chroms
character vector User-given chromosomes that are known to be in diploid state
- classify_allele
logical Whether to only classify allele (internal use only)
- run_hmm
logical Whether to run HMM (internal use only)
- prior
numeric vector Prior probabilities of states (internal use only)
- exclude_neu
logical Whether to exclude neutral segments from retesting (internal use only)
- phasing
logical Whether to use phasing information (internal use only)
- verbose
logical Verbosity