GmmThreshold-class: Output of the 'gmm' method of findThreshold
In shazam: Immunoglobulin Somatic Hypermutation Analysis

GmmThreshold-class

R Documentation

Output of the `gmm` method of findThreshold

GmmThreshold contains output from the gmm method findThreshold. It includes parameters of two Gaussian fits and threshold cut.

## S4 method for signature 'GmmThreshold'
print(x)

## S4 method for signature 'GmmThreshold,missing'
plot(x, y, ...)

`x`	GmmThreshold object
`y`	ignored.
`...`	arguments to pass to plotGmmThreshold.

x: input distance vector with NA or infinite values removed.
model: first-second fit functions.
cutoff: type of threshold cut.
a1: mixing weight of the first curve.
b1: second parameter of the first curve. Either the mean of a Normal distribution or shape of a Gamma distribution.
c1: third parameter of the first curve. Either the standard deviation of a Normal distribution or scale of a Gamma distribution.
a2: mixing weight of the second curve.
b2: second parameter of the second curve. Either the mean of a Normal distribution or shape of a Gamma distribution.
c2: third parameter of the second curve. Either the standard deviation of a Normal distribution or scale of a Gamma distribution.
loglk: log-likelihood of the fit.
threshold: threshold.
sensitivity: sensitivity.
specificity: specificity.
pvalue: p-value from Hartigans' dip statistic (HDS) test. Values less than 0.05 indicate significant bimodality.