preprocessInf {crlmm} | R Documentation

## Preprocessing of Illumina Infinium II arrays.

### Description

This function normalizes the intensities for the 'A' and 'B' alleles for a `CNSet` object and estimates mixture parameters used for subsequent genotyping. See details for how the normalized intensities are written to file. This step is required for subsequent genotyping and copy number estimation.

### Usage

    preprocessInf(cnSet, sampleSheet=NULL, arrayNames = NULL, ids = NULL,
    path = ".", arrayInfoColNames = list(barcode = "SentrixBarcode_A",
    position = "SentrixPosition_A"), highDensity = TRUE, sep = "_", fileExt
    = list(green = "Grn.idat", red = "Red.idat"), XY, anno, saveDate = TRUE, stripNorm
    = TRUE, useTarget = TRUE, mixtureSampleSize = 10^5, fitMixture = TRUE,
    quantile.method="between", eps = 0.1, verbose = TRUE, seed = 1, cdfName)

### Arguments

`cnSet` | object of class `CNSet`
`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.
`XY` | an `NChannelSet` object containing X and Y intensities.
`anno` | data.frame containing SNP annotation information from manifest and additional columns 'isSnp', 'position', 'chromosome' and 'featureNames'. For use when `cdfName`='nopackage'
`saveDate` | 'logical'. Should the dates from each .idat be saved with sample information?
`stripNorm` | 'logical'. Should the data be strip-level normalized?
`useTarget` | 'logical' (only used when `stripNorm=TRUE`). Should the reference HapMap intensities be used in strip-level normalization?
`mixtureSampleSize` | Sample size to be use when fitting the mixture model.
`fitMixture` | 'logical.' Whether to fit per-array mixture model.
`quantile.method` | character string specifying the quantile normalization method to use ('within' or 'between' channels).
`eps` | Stop criteria.
`verbose` | 'logical.' Whether to print descriptive messages during processing.
`seed` | Seed to be used when sampling. Useful for reproducibility
`cdfName` | `character` string indicating which annotation package to load.

### Details

The normalized intensities are written to disk using package `ff` protocols for writing/reading to disk. Note that the object `CNSet` containing the `ff` objects in the `assayData` slot will be updated after applying this function.

### Value

A `ff_matrix` object containing parameters for fitting the mixture model. Note that while the `CNSet` object is not returned by this function, the object will be updated as the normalized intensities are written to disk. In particular, after applying this function the normalized intensities in the `alleleA` and `alleleB` elements of `assayData` are now available.

### Author(s)

R. Scharpf

### See Also

`CNSet-class`, `A`, `B`, `constructInf`, `genotypeInf`, `annotationPackages`

### Examples

    	## See the 'illumina_copynumber' vignette in inst/scripts of
    	## the source package

[Package crlmm version 1.40.0 Index]