cutoff: DEPRECATED, USE fdrControl INSTEAD!

In plbaldoni/mixNBHMM: Differential Peak Calling via Hidden Markov Model With Mixture of Negative Binomial Distributions

Description

For a given FDR control threshold and a set of posterior probabilities, 'cutoff()' classifies genomic windows pertaining to a particular HMM state.

Usage

cutoff(postprob, alpha = 0.05)

Arguments

postprob	numeric vector of posterior probabilities of genomic windows pertaining to a particular HMM state
alpha	FDR threshold (default is 0.05)

Value

A logical vector indicating whether genomic windows pertain to a particular HMM state (TRUE) or not (FALSE), under a given FDR control threshold.

Author(s)

Pedro L. Baldoni, [e-mail]

References

https://biostats.bepress.com/jhubiostat/paper115/

https://doi.org/10.1093/biostatistics/5.2.155

Examples

data(ENCODE)
ENCODE <- createOffset(object = ENCODE,type = 'loess',span = 1)
## Not run: ENCODE <- mixNBHMM(object = ENCODE,control = controlEM())
## Not run: cutoff(metadata(ENCODE)$prob$Differential,alpha = 0.05)

plbaldoni/mixNBHMM documentation built on Dec. 24, 2019, 1:31 p.m.