inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20090128,50K,NMF.R

In ACNE: Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

if (interactive()) savehistory();
library("aroma.affymetrix");
library("ACNE");

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# setup dataset and chip names
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log <- Arguments$getVerbose(-10, timestamp=TRUE);

dataSetName <- "HapMap270,100K,CEU,5trios"
chipType <- "Mapping50K_Hind240"

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# Setup annotation data
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cdf <- AffymetrixCdfFile$byChipType(chipType);
print(cdf);
gi <- getGenomeInformation(cdf);
print(gi);
si <- getSnpInformation(cdf);
print(si);


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# Setup data set
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csR <- AffymetrixCelSet$byName(dataSetName, cdf=cdf);
print(csR);


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# Calibrate and normalize
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acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2");
print(acc);
csC <- process(acc, verbose=log);
print(csC);

bpn <- BasePositionNormalization(csC, target="zero");
print(bpn);
csN <- process(bpn, verbose=log);
print(csN);


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# Summarize replicated probes
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plm <- NmfSnpPlm(csN, mergeStrands=TRUE);
print(plm);
fit(plm, verbose=log);

ces <- getChipEffectSet(plm);
print(ces);


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# Fragment-length normalization
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fln <- FragmentLengthNormalization(ces, target="zero");
print(fln);
cesN <- process(fln, verbose=log);
print(cesN);



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# Segmentation
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# CBS needs theta = thetaA + thetaB
as <- AlleleSummation(cesN);
cesT <- process(as, verbose=log);
cbs <- CbsModel(cesT);
print(cbs);
ce <- ChromosomeExplorer(cbs);
print(ce);

process(ce, chromosomes=1:5, verbose=log);