readIdatFiles {crlmm} | R Documentation

## Reads Idat Files from Infinium II Illumina BeadChips

### Description

Reads intensity information for each bead type from .idat files of Infinium II genotyping BeadChips

### Usage

    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)

### Arguments

`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?
`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.

### Author(s)

Matt Ritchie

### References

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.

### Examples

    #RG = readIdatFiles()

[Package crlmm version 1.38.0 Index]