Multi-Patient Analysis of Genomic Markers


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Documentation for package ‘MPAgenomics’ version 1.2.3

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MPAgenomics-package Multi-Patient Analysis of Genomic Markers
MPAgenomics-package, Multi-Patient Analysis of Genomic Markers
addChipType Add a new chip type to the existing aroma architecture
addData Add a new data-set to the existing aroma architecture
callingObject Create the list of parameters for callingProcess function
callingProcess Calling aberrations in segmented copy-number signal.
CNAobjectToCGHcallObject Convert CNAobject
cnSegCallingProcess Segment a copy-number signal and call the found segments.
createArchitecture Create aroma architecture and copy files
createEmptyArchitecture Create aroma architecture
filterSeg Filter segments
findPlateau Find the best choice of segmentation parameter.
getCopyNumberSignal Extract copy-number signal from aroma files
getFracBSignal Extract allele B fraction signal from aroma files
getGenotypeCalls Extract genotype calls from aroma files
getListOfFiles Get the contents of a data folder
getSymFracBSignal Extract symmetrized allele B fraction signal from aroma files
HDlarsbivariate lars algorithm for bivariate signal
markerSelection markers selection
MPAgenomics Multi-Patient Analysis of Genomic Markers
segFracBSignal segmentation function for the allele B fraction
segmentation segmentation function
segmentationAroma segmentation function
segmentationObject Create the list of parameters for segmentation function
SignalNormalization Normalization process
signalPreProcess Normalization process
symmetrizeFracB symmetrize an allele B fraction signal
variableSelection SNPs selection