BioGAIL R Packages

R Package for Datamining

At term, the purpose of the "dm" package is to offer an unified framework of datamining tools. In its current realease, it include the following facilities:

• Reading and writing of .arff files (WEKA format) via functions read.arff() and write.arff().
• SMO algorithm to solve Support Vector Machine (SVM) problems, with user defined kernels. This is done by function smoSolver() which take as input the Gram matrix of training instances and solve the maximal margin hyperplane problem. One can also used smo() and predict.smo() for extended functionalities.
• Kernel functions: polynomial.kernel()
• Attribut ranking by Support Vector Machine Ranking with linear machines or LogRatio machines (see function svmRank()).
• Recursive Feature Elimination Ranking via rfeRank(). When used in combination with svmRank(), one can build an svmRfe attribut ranking.
• Splitting of a dataset into stratified folds (see stratifiedSplit())

Download: dm_3.3.tar.gz

Contact: julien.prados@cui.unige.ch

R Package for Mass Spectrometry

The "ms" package contains functions to process mass spectrometry data. It contains:

• Sliding windows filtering and smoothing functions for 1D signals: avgfilt(), closefilt(), percfilt(), sdfilt()
• Peak detection functions for 1D, 2D, nD signals: valleys(), valleys2D(), valleysGraph()
• A method to build delaunay triangulation graph of a set of 2D points: delaunay()
• A linear model fitting method on 1D peakslmPeakFit()
• A peak alignement/clustering method mzcl()
• A function for hierachical clustering comparison hclustdiff()
• An utility function to compute areas of triangles triangle.area()

Contact: julien.prados@cui.unige.ch