readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path="", arrayInfoColNames=list(barcode="SentrixBarcode_A", position="SentrixPosition_A"), highDensity=FALSE, sep="_", fileExt=list(green="Grn.idat", red="Red.idat"), saveDate=FALSE, verbose=FALSE)
data.frame
containing Illumina sample sheet
information (for required columns, refer to BeadStudio Genotyping
guide - Appendix A).NULL
, all arrays that can be found in the
specified working directory will be read in.NULL
all probes found on the first array are read in.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")
sampleSheet
is
specified). If TRUE
, array extensions '\_A', '\_B' in
sampleSheet are replaced with 'R01C01', 'R01C02' etc.R
, G
), and indicator
for SNPs with 0 beads (zero
) for each bead type.
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.