Usage
BMIQ(beta.v, design.v, doH = TRUE, nfit = 50000, th1.v = c(0.2, 0.75), th2.v = NULL, niter = 5, tol = 0.001)
Arguments
beta.v
double vector consisting of beta values. Missing values (NAs) cannot be handled, so
these must be removed or imputed prior to running BMIQ. Before normalization, beta values that are
exactly 0 and exactly 1 are replaced by the minimum positive and maximum value below 1, respectively.
design.v
integer vector of length length(beta.v), containing the values 1 and 2
only. These values specify probe design type.
doH
Flag indicating if normalization for hemimethylated type II probes is to be performed.
nfit
Number of probes of a given design to use for the fitting. Smaller values will make BMIQ faster at
the expense of accuracy. Values between 10000 and 50000 seem to work well.
th1.v
Thresholds "type 1" to use for the initialization of the EM algorithm. These values should represent
best guesses for calling type I probes hemi-methylated and methylated, and are refined in further
steps by the algorithm.
th2.v
Thresholds "type 2" to used for the initialization of the EM algorithm. These values should represent
best guesses for calling type II probes hemi-methylated and methylated, and are refined in further
steps by the EM algorithm. If this is NULL (default), the thresholds are estimated based on
th1.v and a modified PBC correction method.
niter
Maximum number of EM iterations to be performed.
tol
Tolerance threshold for EM algorithm.