Processing and Classification of Protein Mass Spectra (SELDI) Data

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Documentation for package `caMassClass' version 1.0

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base64decode Convert R vectors to/from the Base64 format
base64encode Convert R vectors to/from the Base64 format
bin2raw Convert R vectors to/from the raw binary format
colAUC Columnwise Area Under ROC Curve (AUC)
combs All Combinations of k Elements from Vector v
EndRule Moving Window Analysis of a Vector
LogitBoost LogitBoost Classification Algorithm
msc.baseline.subtract Baseline Subtraction for Mass Spectra Data
msc.biomarkers.fill Fill Empty Spaces in Biomarker Matrix
msc.biomarkers.read.csv Read and Write biomarker matrix in CSV format
msc.biomarkers.write.csv Read and Write biomarker matrix in CSV format
msc.classifier.run Train and Test Chosen Classifier.
msc.classifier.test Test a Classifier through Cross-validation
msc.copies.merge Merge Multiple Copies of Mass Spectra Samples
msc.features.remove Remove Highly Correlated Features
msc.features.scale Scale Classification Data
msc.features.select Reduce Number of Features Prior to Classification
msc.mass.adjust Perform Normalization and Mass Drift Adjustment for Mass Spectra Data.
msc.mass.cut Remove Low Mass Portion of the Mass Spectra Data.
msc.msfiles.read.csv Read Protein Mass Spectra from CSV files
msc.peaks.align Align Peaks of Mass Spectra into a "Biomarker" Matrix
msc.peaks.alignment Align Peaks of Mass Spectra into a "Biomarker" Matrix
msc.peaks.clust Clusters Peaks of Mass Spectra
msc.peaks.find Find Peaks of Mass Spectra
msc.peaks.read.csv Read and Write Mass Spectra Peaks in CSV Format
msc.peaks.write.csv Read and Write Mass Spectra Peaks in CSV Format
msc.preprocess.run Preprocessing Pipeline of Protein Mass Spectra
msc.project.read Read and Manage a Batch of Protein Mass Spectra
msc.project.run Read and Preprocess Protein Mass Spectra
msc.sample.correlation Sample Correlation
msc.sample.split Split Data into Test and Train Set
predict.LogitBoost Prediction Based on LogitBoost Classification Algorithm
raw2bin Convert R vectors to/from the raw binary format
read.ENVI Read and write binary data in ENVI format
runmad Moving Window Analysis of a Vector
runmax Moving Window Analysis of a Vector
runmean Moving Window Analysis of a Vector
runmin Moving Window Analysis of a Vector
runquantile Moving Window Analysis of a Vector
trapz Trapezoid Rule Numerical Integration
write.ENVI Read and write binary data in ENVI format