Reads intensity information for each bead type from a single IDAT file for Infinium II, Infinium HD and expression platforms.
character string specifying IDAT file to be read in.
This allows the return of parts of the IDAT file, see Value. This argument is only supported for non-encrypted IDAT files; setting it to be different from default on an encrypted file throws an error.
This function returns a list containing summarized intensities and other information extracted from a single IDAT file.
Thanks to Keith Baggerly for providing the first version of this code.
There are two commonly encountered versions of IDAT. One version uses encryption to store data and is the format usually produced by Illumina expression arrays. The other version is unencrypted files and is found in data from SNP arrays and DNA methylation arrays.
This function is able to handle data in either format, scanning the file header and calling the appropriate reading routine internally.
The function supports reading gzipped, unencrypted IDAT files.
The use of the
what argument is for package writers.
The exact data returned will vary depending upon whether the input file was encrypted or not. In either case, everything that can be extract from the file will be returned in the form of a list.
For both file types the most important entry in the returned list is the
Quants. When reading unencrypted files this contains average intensity (
number of beads (
NBeads) and a measure of variability
SD) for each bead type on the array. For expression arrays
in addition to these some additional information is available,
including median and trimmed-mean estimates of average intensity,
averaged local background intensities and the number of beads present
before outliers where excluded.
For both file types details of scanning and decoding dates are
included in the
A further list entry,
Extra, may also be present. Occasionally an field
in the IDAT file will have a number of data points inconsistent with the remainder
of the file and as such is not returned in the
Quants entry. Such
fields will be placed here. So far only the HumanHap550 v1 BeadChip has exhibited
what is set to
nSNPsRead the function returns an
integer equal to this field. In case
what is set to
IlluminaID the function returns a character vector containing
Unencrypted: Keith Baggerly, with modifications by Matt Ritchie, Henrik Bengtsson and Kasper Daniel Hansen. Encrypted: Mike Smith
Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'e S, Irizarry RA. R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics. 2009 Oct 1;25(19):2621-3.
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