constructInf {crlmm} | R Documentation

## Instantiate an object of class CNSet for the Infinium platforms.

### Description

Instantiates an object of class CNSet for the Infinium platforms. Elements of `assayData` and `batchStatistics` will be `ff` objects. See details.

### Usage

    constructInf(sampleSheet = NULL, arrayNames = NULL, path = ".",
           arrayInfoColNames = list(barcode="SentrixBarcode_A",position="SentrixPosition_A"), highDensity = FALSE, sep = "_",
           fileExt = list(green = "Grn.idat", red = "Red.idat"), XY, cdfName, anno, genome, verbose = FALSE, batch=NULL, saveDate = TRUE)

### 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.
`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` containing X and Y intensities.
`cdfName` | annotation package (see also `validCdfNames`) or 'nopackage' when an `anno` data.frame and `genome` supplied
`anno` | data.frame containing SNP annotation information from manifest and additional columns 'isSnp', 'position', 'chromosome' and 'featureNames'. For use when `cdfName`='nopackage'
`genome` | character string specifying which genome is used in annotation
`verbose` | 'logical.' Whether to print descriptive messages during processing.
`batch` | batch variable. See details.
`saveDate` | 'logical'. Should the dates from each .idat be saved with sample information?

### Details

This function initializes a container for storing the normalized intensities for the A and B alleles at polymorphic loci and the normalized intensities for the 'A' allele at nonpolymorphic loci. CRLMM genotype calls and confidence scores are also stored in the assayData. This function does not do any preprocessing or genotyping – it only creates an object of the appropriate size. The initialized values will all be 'NA'.

The ff package provides infrastructure for accessing and writing data to disk instead of keeping data in memory. Each element of the `assayData` and `batchStatistics` slot are ff objects. ff objects in the R workspace contain pointers to several files with the '.ff' extension on disk. The location of where the data is stored on disk can be specified by use of the `ldPath` function. Users should not move or rename this directory. If only output files are stored in `ldPath`, one can either remove the entire directory prior to rerunning the analysis or all of the '.ff' files. Otherwise, one would accumulate a large number of '.ff' files on disk that are no longer in use.

We have adopted the `ff` package in order to reduce crlmm's memory footprint. The memory usage can be fine-tuned by the utilities `ocSamples` and `ocProbesets` provided in the `oligoClasses` package. In most instances, the user-level interface will be no different than accessing data from ordinary matrices in R. However, the differences in the underlying representation can become more noticeable for very large datasets in which the I/O for accessing data from the disk can be substantial.

### Value

A `CNSet` object

### Author(s)

R. Scharpf

### See Also

`ldPath`, `ocSamples`, `ocProbesets`, `CNSet-class`, `preprocessInf`, `genotypeInf`

### Examples

    ## See the Illumina vignettes in inst/scripts of the
    ## source package for an example

[Package crlmm version 1.45.0 Index]