caMassClass-package {caMassClass} | R Documentation |
Functions for processing and classification of protein mass spectra data. Includes support for I/O in mzXML and CSV formats.
Package: | caMassClass |
Version: | 1.5 |
Date: | 2006-04-11 |
Depends: | R (>= 2.0.0), PROcess, e1071, nnet, rpart, caTools, XML, digest |
License: | The caMassClass Software License, Version 1.0 (See COPYING file |
or http://ncicb.nci.nih.gov/download/camassclasslicense.jsp) | |
URL: | http://ncicb.nci.nih.gov/download/index.jsp |
Index of Preprocessing Functions:
msc.project.read | Read and Manage a Batch of Protein Mass Spectra |
msc.project.run | Read and Preprocess Protein Mass Spectra |
msc.preprocess.run | Preprocessing Pipeline of Protein Mass Spectra |
msc.baseline.subtract | Baseline Subtraction for Mass Spectra Data |
msc.mass.cut | Remove Low Mass Portion of the Mass Spectra Data. |
msc.mass.adjust | Perform Normalization and Mass Drift Adjustment |
msc.peaks.find | Find Peaks of Mass Spectra |
msc.peaks.clust | Clusters Peaks of Mass Spectra (low level) |
msc.peaks.align | Align Peaks of Mass Spectra into Biomarker Matrix |
msc.biomarkers.fill | Fill Empty Spaces in Biomarker Matrix |
msc.copies.merge | Merge Multiple Copies of Mass Spectra Samples |
msc.sample.correlation | Sample Correlation (low level) |
Index of Classification Functions:
msc.classifier.test | Test a Classifier through Cross-validation |
msc.features.remove | Remove Highly Correlated Features |
msc.features.scale | Scale Classification Data |
msc.features.select | Reduce Number of Features Prior to Classification |
msc.classifier.run | Train and Test Chosen Classifier. |
Index of I/O Functions:
msc.rawMS.read.csv | Read Protein Mass Spectra from CSV files |
msc.rawMS.read.mzXML | Read raw Mass Spectra from mzXML Files |
msc.rawMS.write.mzXML | Write raw Mass Spectra to mzXML Files |
msc.peaks.read.csv | Read Mass Spectra Peaks in CSV Format |
msc.peaks.write.csv | Write Mass Spectra Peaks in CSV Format |
msc.peaks.read.mzXML | Read peaks heights and positions from mzXML File |
msc.peaks.write.mzXML | Write peaks heights and positions to mzXML File |
msc.biomarkers.read.csv | Read biomarker matrix in CSV format |
msc.biomarkers.write.csv | Write biomarker matrix in CSV format |
msc.project.read | Read and Manage a Batch of Protein Mass Spectra Data |
read.mzXML | Read mzXML Files into generic data structure |
write.mzXML | Write mzXML Files from generic data structure |
Jarek Tuszynski <jaroslaw.w.tuszynski@saic.com>
See additional documentation in "R/library/caMassClass/doc" directory.
Se also Packages: PROcess (http://www.bioconductor.org/packages/bioc/1.8/html/PROcess.html), xcms (http://www.bioconductor.org/packages/bioc/1.8/html/xcms.html), ppc (CRAN).