readIllumina(dir = ".", useImages = FALSE, illuminaAnnotation = NULL, sectionNames = NULL, metricsFile = "Metrics.txt", forceIScan = FALSE, dec = ".", sampleSheet="sampleSheet.csv",...)beadLevelData-class
If present, the function will automatically read the following files from the directory
.txt Text file that lists the ID, coordinates and intensity for every decoded bead on an array section. The intensities have been subjected to a local background correction. If useImages = FALSE these intensities will be used as a starting point for analysis
.sdf Illumina\'s Sample Description File for the entire chip or SAM. This is used within beadarray to determine the physical properties of a section.
.locs Locations of all beads on the array (i.e. including all those that could not be decoded)
Metrics.txt Illumina\'s metrics that are produced at the time of scanning. Identification of the Metrics file is defined by the metricsFile argument. Internally, this argument is passed to grep. The default will thus find other items such as "Metrics.txt2" or "OtherMetrics.txt". To avoid these being read you can use a more specific regex such as "^Metrics.txt$".
Separate functionality exists to read and manipulate TIFF images that may be found in the same directory. See readTIFF.
If useImage is set to TRUE, intensities are extracted from the TIFF images using the bead-centre coordinates provided in the text file. Foreground values are calculated from a sharpened version of the image as described in Kuhn et al. Background values are calculated as the median of the 5 lowest pixels in a 17x17 pixel square around the bead-centre, detailed in Smith et al.