constructInf: Instantiate an object of class CNSet for the Infinium...

In benilton/crlmm-release: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

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, 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)
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

benilton/crlmm-release documentation built on May 12, 2019, 10:59 a.m.