CNVassoc-internal: Internal CNVassoc functions

In isglobal-brge/CNVassoc: Association analysis of CNVs and imputed SNPs incorporating uncertainty

Description

Internal CNVassoc functions

Usage

assocCNV.i(x, formula, num.copies, cnv.tol, ...)
EMlogistic(y, X, w, beta, tol = 10^-6, max.iter = 1000, verbose = FALSE)
EMnorm(y, X, w, beta, sigma, variant, tol = 10^-6, max.iter = 1000, 
verbose = FALSE)
EMpoisson(y, X, w, beta, tol = 10^-6, max.iter = 1000, verbose = FALSE)
EMWeibull(y, cens, X, w, beta, alpha, tol = 10^-6, max.iter = 1000, 
verbose = FALSE)
hessianLinear(beta, sigma, y, w, X, variant)
hessianLogistic(beta, y, w, X, variant)
hessianPoisson(beta, y, w, X, variant)
hessianWeibull(beta, alpha, y, cens, w, X, variant)
ifelsem(test, yes, no)
linear.fit(x, y, weights, tol = 1e-08, max.iter = 25, verbose = FALSE)
logistic.fit(x, y, weights, tol = 1e-08, max.iter = 25, verbose = FALSE)
matrix2vector(betam, variant)
mix(mixdat, method, num.class, mean.ini, sigma.ini, pi.ini, var.equal)
mixture(intensities, num.class, mix.method, threshold.0, threshold.k, mu.ini,
            sigma.ini, pi.ini, var.equal)
NRlogistic(y, X, w, beta, variant, tol, max.iter, verbose)
NRnorm(y, X, w, beta, sigma, variant, tol = 10^-6, max.iter = 1000, 
verbose = FALSE)
plot.cnv.intensities(x, my.colors = c("black", "red", "blue"), 
ylab = "Peak Intensity", 
            xlab = c("individuals", "Phenotype"), case.control, cex.leg = 0.8, 
            dens.bw = "nrd0", dens.adjust = 1, ...)
plot.cnv.probabilities(x, my.colors = c("black", "red", "blue"), case.control, 
            ylab = "CNV probability", xlab, ...)
vector2matrix(betav, variant, J)
is.quantitative(formula, data)
getProbsRegions.i(i, blocks, probs, annotation, nclass)
plapply(X, FUN, ...)
translate(obj)

Details

These are not to be called by the user

Value

Internal functions

Examples

data(dataMLPA)
CNV  <-  cnv(x  =  dataMLPA$Gene2,  threshold.0  =  0.01,  
                mix.method  =  "mixdist")
modmul  <-  CNVassoc(casco  ~  CNV,  data  =  dataMLPA,  model  =  "mul")
modmul
summary(modmul)
anova(modmul,update(modmul,model="add"))
logLik(modmul)

isglobal-brge/CNVassoc documentation built on May 30, 2019, 9:48 p.m.