read.SnpSetIllumina(samplesheet, manifestpath=NULL, reportpath=NULL, rawdatapath=NULL, reportfile=NULL, briefOPAinfo=TRUE, readTIF=FALSE, nochecks=FALSE, sepreport="\t", essentialOnly=FALSE, ...)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 slotbeadarray package and raw TIF files to
read dataTRUE then only the essential
columns from a reportfile are included into the result. See detailsreadIllumina
and can be used to perform bead-level normalizationSnpSetIllumina object, or a MultiSet object
when nochecks is TRUE.
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.
Zero values in the raw data signals are set to NA
Ideally the OPA manifest file containing SNP annotation should be available,
these files are provided by Illumina. Columns ‘IllCode’,
‘CHR’, and ‘MapInfo’ are put into the
featureData slot.
GenCall Data
In order to process experiments that were genotyped using the GenCall software,
the arrays should be scanned with the setting
true 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.
BeadStudio Data
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, or columns in the featureData slot if
values are identical for all samples in the reportfile.
When nochecks is TRUE then only the ‘SNP Name’ and
‘Sample ID’ columns are required. The resulting object is now of
class MultiSet
Sample sheets
To help generate a sample sheet for BeadStudio data a Sample_Map.txt
file can be converted to a sample sheet with the
Sample_Map2Samplesheet function. For Beadstudio reportfiles it is
also possible to set samplesheet=NULL. In this case the phenoData
slot will be fabricated from the sample names in the reportfile.
Manifest/OPA/annotation files
For BeadStudio reportfiles it is not necessary to have a Manifest file if the
columns ‘Chr’ and ‘Position’ are available in the
report file. Currently this is the only way to import data from Infinium
arrays, because Illumina does not supply Manifest files for these arrays.
SnpSetIllumina-class, Sample_Map2Samplesheet,
readIllumina
# 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)
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