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MPAgenomics (version 1.2.3)

Multi-Patient Analysis of Genomic Markers

Description

Preprocessing and analysis of genomic data. 'MPAgenomics' provides wrappers from commonly used packages to streamline their repeated manipulation, offering an easy-to-use pipeline. The segmentation of successive multiple profiles is performed with an automatic choice of parameters involved in the wrapped packages. Considering multiple profiles in the same time, 'MPAgenomics' wraps efficient penalized regression methods to select relevant markers associated with a given outcome. Grimonprez et al. (2014) .

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Version

Install

install.packages('MPAgenomics')

Monthly Downloads

68

Version

1.2.3

License

GPL (>= 2)

Maintainer

Samuel Blanck

Last Published

March 30th, 2021

Functions in MPAgenomics (1.2.3)

markerSelection

markers selection
getCopyNumberSignal

Extract copy-number signal from aroma files
filterSeg

Filter segments
getGenotypeCalls

Extract genotype calls from aroma files
findPlateau

Find the best choice of segmentation parameter.
createEmptyArchitecture

Create aroma architecture
getFracBSignal

Extract allele B fraction signal from aroma files
segFracBSignal

segmentation function for the allele B fraction
segmentationAroma

segmentation function
getSymFracBSignal

Extract symmetrized allele B fraction signal from aroma files
SignalNormalization

Normalization process
segmentation

segmentation function
getListOfFiles

Get the contents of a data folder
signalPreProcess

Normalization process
symmetrizeFracB

symmetrize an allele B fraction signal
segmentationObject

Create the list of parameters for segmentation function
variableSelection

SNPs selection
CNAobjectToCGHcallObject

Convert CNAobject
callingObject

Create the list of parameters for callingProcess function
addData

Add a new data-set to the existing aroma architecture
addChipType

Add a new chip type to the existing aroma architecture
cnSegCallingProcess

Segment a copy-number signal and call the found segments.
HDlarsbivariate

lars algorithm for bivariate signal
MPAgenomics-package

Multi-Patient Analysis of Genomic Markers
callingProcess

Calling aberrations in segmented copy-number signal.
createArchitecture

Create aroma architecture and copy files