read.SnpSetIllumina {beadarraySNP}R Documentation

Read Experimental Data and into an 'SnpSetIllumina' Object

Description

A SnpSetIllumina object is created from the textfiles created by the Illumina GenCall or BeadStudio software.

Usage

   read.SnpSetIllumina(samplesheet, manifestpath = NULL, reportpath = NULL,
     rawdatapath = NULL, reportfile = NULL, briefOPAinfo=TRUE, verbose=FALSE)

Arguments

samplesheet a data.frame or filename, contains the sample sheet
manifestpath a character string for the path containing the manifests / OPA definition files, defaults to path of samplesheet
reportpath a character string for the path containing the report files, defaults to path of samplesheet
rawdatapath a character string for the path containing the intensity data files, defaults to path of samplesheet
reportfile a character string for the name of BeadStudio reportfile
briefOPAinfo logical, if TRUE then only the SNP name, Illumi code, chromosome and basepair position are put into the featureData slot of the result, else all information from the OPA file is put into the featureData slot
verbose logical, if TRUE then some extra information is given during the import

Details

The text files from Illumina software are imported to a SnpSetIllumina object. Both result files from GenCall and BeadStudio can be used. In both cases the sample sheets from the experiments are used to select the proper data from the report or data files. The following columns from the sample sheet file are used for this purpose: 'Sample_Name', 'Sentrix_Position', and 'Pool_ID'. The values in columns 'Sample_Plate', 'Pool_ID', and 'Sentrix_ID' should be the same for all samples in the file, as this is the case for processed experiments. The contents of the sample sheet are put into the phenoData slot. Also the OPA definition file containing SNP annotation should be available, these files are provided by Illumina. Columns 'IllCode', 'CHR', and 'MapInfo' are put into the featureData slot.

In order to process experiments that were genotyped using the GenCall software, the arrays should be scanned with the setting <SaveTextFiles>true</SaveTextFiles> in the Illumina configuration file Settings.XML. 3 Types of files need to be present in the same folder: The sample sheet, .csv files containing signal intensity data, and the report file that contains the genotype information. For each sample in the sample sheet there should be a .csv file with the following file mask: [sam_id]_R00[yy]_C00[xx].csv, where sam_id is the Illumina ID for the SAM, and xx and yy are the column and row number respectively. From the report files the file with mask [Pool_ID]_LocusByDNA[_ExpName].csv is used. 'Pool_ID' is the OPA panel used, and '_ExpName' is optional.

To process experiments that were processed with BeadStudio, only two files are needed. The sample sheet and the Final Report file. The sample sheet must contain the same columns as for GenCall, the report file should contain the following columns: 'SNP Name', 'Sample ID', 'GC Score', 'Allele1 - AB', 'Allele2 - AB', 'GT Score', 'X Raw', and 'Y Raw'. 'SNP Name' and 'Sample ID' are used to form rows and columns in the experimental data, 'GC Score' is put in the callProbability matrix, 'Allele1 - AB' and 'Allele2 - AB' are combined into the call matrix, 'GT Score' is added to the featureData slot, 'X Raw' is put in the R matrix and 'Y Raw' in the G matrix. Other columns in the report file are added as matrices in the assayData slot.

Value

This function returns an SnpSetIllumina object.

Author(s)

Jan Oosting

See Also

SnpSetIllumina-class

Examples

# read a SnpSetIllumina object using example textfiles in data directory
datadir <- system.file("testdata", package="beadarraySNP")
SNPdata <- read.SnpSetIllumina(paste(datadir,"4samples_opa4.csv",sep="/"),datadir)

[Package beadarraySNP version 1.0.0 Index]