This function normalizes the intensities for the 'A' and 'B'
alleles for a CNSet object and estimates mixture
parameters used for subsequent genotyping. See details for
how the normalized intensities are written to file. This step
is required for subsequent genotyping and copy number
estimation.
data.frame containing Illumina sample sheet
information (for required columns, refer to BeadStudio Genotyping
guide - Appendix A).
arrayNames
character vector containing names of arrays to be
read in. If NULL, all arrays that can be found in the
specified working directory will be read in.
ids
vector containing ids of probes to be read in. If
NULL all probes found on the first array are read in.
path
character string specifying the location of files to be
read by the function
arrayInfoColNames
(used when sampleSheet is specified)
list containing elements 'barcode' which indicates column names in
the sampleSheet which contains the arrayNumber/barcode number
and 'position' which indicates the strip number. In older style
sample sheets, this information is combined (usually in a column
named 'SentrixPosition') and this should be specified as
list(barcode=NULL, position="SentrixPosition")
highDensity
logical (used when sampleSheet is
specified). If TRUE, array extensions '_A', '_B' in
sampleSheet are replaced with 'R01C01', 'R01C02' etc.
sep
character string specifying separator used in .idat file
names.
fileExt
list containing elements 'Green' and 'Red' which
specify the .idat file extension for the Cy3 and Cy5 channels.
XY
an NChannelSet object containing X and Y intensities.
saveDate
'logical'. Should the dates from each .idat be saved
with sample information?
stripNorm
'logical'. Should the data be strip-level normalized?
useTarget
'logical' (only used when stripNorm=TRUE).
Should the reference HapMap intensities be used in strip-level normalization?
mixtureSampleSize
Sample size to be use when fitting the mixture model.
fitMixture
'logical.' Whether to fit per-array mixture
model.
quantile.method
character string specifying the quantile normalization method to use ('within' or 'between' channels).
eps
Stop criteria.
verbose
'logical.' Whether to print descriptive messages during processing.
seed
Seed to be used when sampling. Useful for
reproducibility
cdfName
character string indicating which annotation
package to load.
Details
The normalized intensities are written to disk using package
ff protocols for writing/reading to disk. Note that the
object CNSet containing the ff objects in the
assayData slot will be updated after applying this
function.
Value
A ff_matrix object containing parameters for fitting the
mixture model. Note that while the CNSet object is not
returned by this function, the object will be updated as the
normalized intensities are written to disk. In particular,
after applying this function the normalized intensities in the
alleleA and alleleB elements of assayData
are now available.
Author(s)
R. Scharpf
See Also
CNSet-class, A, B,
constructInf, genotypeInf, annotationPackages
Examples
## See the 'illumina_copynumber' vignette in inst/scripts of
## the source package