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.
saveDate
logical. Should the dates from each .idat be saved
with sample information?
verbose
logical. Should processing information be displayed as data is read in?
Details
The summarised Cy3 (G) and Cy5 (R) intensities (on the orginal scale)
are read in from the .idat files.
Where available, a sampleSheet data.frame, in the same format
as used by BeadStudio (columns 'Sample_ID', 'SentrixBarcode_A' and
'SentrixPosition_A' are required) which keeps track of sample
information can be specified.
Thanks to Keith Baggerly who provided the code to read in the binary .idat files.
Value
NChannelSet with intensity data (R, G), and indicator
for SNPs with 0 beads (zero) for each bead type.