caMassClass-package {caMassClass}R Documentation

Processing and Classification of Protein Mass Spectra Data

Description

Functions for processing and classification of protein mass spectra data. Includes support for I/O in mzXML and CSV formats.

Details

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

Author(s)

Jarek Tuszynski <jaroslaw.w.tuszynski@saic.com>

See Also

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).


[Package caMassClass version 1.6 Index]