Usage
BMIQ(beta.v, design.v, nL = 3, doH = TRUE, nfit = 50000, th1.v = c(0.2, 0.75), th2.v = NULL, niter = 5, tol = 0.001, plots = TRUE, sampleID = 1, pri=TRUE)
"BMIQ"(beta.v, nL=3, doH=TRUE, nfit=5000, th1.v=c(0.2,0.75), th2.v=NULL, niter=5, tol=0.001, plots=FALSE, pri=FALSE )
CheckBMIQ(beta.v, design.v, pnbeta.v)
Arguments
beta.v
vector consisting of beta-values for a given sample, or a MethyLumiSet or MethylSet containing multiple samples. For the MethyLumiSet and MethylSet methods, this is the only required argument, and the function will be run on each sample.
design.v
corresponding vector specifying probe design type (1=type1,2=type2). This must be of the same length as beta.v and in the same order.
nL
number of states in beta mixture model. 3 by default. At present BMIQ only works for nL=3.
doH
perform normalisation for hemimethylated type2 probes. These are normalised using an empirical conformal transformation and also includes the left-tailed type2 methylated probes since these are not well described by a beta distribution. By default TRUE.
nfit
number of probes of a given design type to use for the fitting. Default is 50000. Smaller values (~10000) will make BMIQ run faster at the expense of a small loss in accuracy. For most applications, 5000 or 10000 is ok.
th1.v
thresholds used for the initialisation of the EM-algorithm, they should represent buest guesses for calling type1 probes hemi-methylated and methylated, and will be refined by the EM algorithm. Default values work well in most cases.
th2.v
thresholds used for the initialisation of the EM-algorithm, they should represent buest guesses for calling type2 probes hemi-methylated and methylated, and will be refined by the EM algorithm. By default this is null, and the thresholds are estimated based on th1.v and a modified PBC correction method.
niter
maximum number of EM iterations to do. This number should be large enough to yield good fits to the type1 distribution. By default 5.
tol
tolerance convergence threshold for EM algorithm. By default 0.001.
plots
logical specifying whether to plot the fits and normalised profiles out. By default TRUE.
sampleID
the ID of the sample being normalised.
pri
logical: print verbose progress information?
pnbeta.v
BMIQ normalised profile.