Usage
ClusProc(signal, N = 2:6, varSelection = c("PC1", "RAW", "PC.9", "MEAN"), threshold = 1e-05, itermax = 8, adjust = TRUE, thresMAF = 0.01, scale = FALSE, thresSil = 0.01)
Arguments
signal
The matrix of intensity measurements. The
row names must be consistent with the Individual ID in
fam file.
N
Number of clusters one wants to fit to the data.
N needs to be larger than 1 and if it is 1, error will be
returned. The default value 2,3,...,6 will be used if it
is missing.
varSelection
Factor. For specifying how to handle
the intensity values. It must take value on 'RAW',
'PC.9', 'PC1'and 'MEAN'. If the value is 'RAW', then the
raw intensity value will be used. If it is 'PC.9', then
the first several PCA scores which account for 90% of
all the variance will be used. If the value is 'PC1',
then the first PCA scores will be used. If the value is
'MEAN', the mean of all the probes will be used. The
default method is 'PC1'.
threshold
Optional number of convergence
threshold. The iteration stops if the absolute difference
of log likelihood between successive iterations is less
than it. The default threshold 1e-05 will be used if it's
missing.
itermax
Optional. The iteration stops if the time
of iteration is large than this value. The default number
8 will be used if it's missing.
adjust
Logicals, If TRUE (default), the result
will be adjusted by the silhouette score. See details.
thresMAF
The minor allele frequency threshold.
thresSil
The abandon threshold. The individual
whose silhouette score is smaller than this value will be
abandoned.
scale
Logicals. If TRUE, the signal will be scale
by using sample mean and sample variance by columns
before further data-processing.