readIdatFiles {crlmm} | R Documentation |
Reads intensity information for each bead type from .idat files of Infinium II genotyping BeadChips
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)
sampleSheet |
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? |
The summarised Cy3 (G) and Cy5 (R) intensity, number of beads that were used in each channel and standard errors (all 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.
NChannelSet with intensity data (R
, G
), number of beads
(Rnb
, Gnb
) and standard errors (Rse
, Gse
)
for each bead type.
Matt Ritchie
#RG = readIdatFiles()