Package: ramwas 1.37.0

Andrey A Shabalin

ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) <doi:10.1093/bioinformatics/bty069>.

Authors:Andrey A Shabalin [aut, cre], Shaunna L Clark [aut], Mohammad W Hattab [aut], Karolina A Aberg [aut], Edwin J C G van den Oord [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ramwas/json (API)

# Install 'ramwas' in R:
install.packages('ramwas', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/andreyshabalin/ramwas/issues

On BioConductor:ramwas-1.37.0(bioc 3.24)ramwas-1.36.0(bioc 3.23)

dnamethylationsequencingqualitycontrolcoveragepreprocessingnormalizationbatcheffectprincipalcomponentdifferentialmethylationvisualization

4.26 score 10 stars 91 scripts 466 downloads 55 exports 89 dependencies

Last updated from:df845e91c1. Checks:2 ERROR, 11 WARNING, 1 OK. Indexed: yes.

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bioc-checksERROR265
linux-devel-arm64WARNING323
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source / vignettesERROR486
linux-release-arm64WARNING326
linux-release-x86_64WARNING404
macos-release-arm64WARNING336
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macos-oldrel-arm64WARNING256
macos-oldrel-x86_64WARNING480
windows-develWARNING516
windows-releaseWARNING472
windows-oldrelWARNING474
wasm-releaseOK199

Exports:cachedRDSloadcolSumsSqestimateFragmentSizeDistributionfindBestNpvsgetCpGsetALLgetCpGsetCGgetDataByLocationgetLocationsgetMWASgetMWASandLocationsgetMWASrangeinjectSNPsMAFinsilicoFASTQisAbsolutePathmadeBEDmadeBEDgraphmadeBEDgraphRangemadeBEDrangemakefullpathmanPlotFastmanPlotPreparemat2colsorthonormalizeCovariatesparameterDumpparameterPreprocessparametersFromFilepipelineProcessBamplotCVcorsplotFragmentSizeDistributionEstimateplotPCvaluesplotPCvectorsplotPredictionplotROCprocessCommandLinepvalue2qvalueqcmeanqqPlotFastqqPlotPrepareramwas0createArtificialDataramwas1scanBamsramwas2collectqcramwas3normalizedCoverageramwas4PCAramwas5MWASramwas6annotateTopFindingsramwas7ArunMWASesramwas7BrunElasticNetramwas7CplotByNCpGsramwas7riskScoreCVramwasAnnotateLocationsramwasParametersramwasSNPsrowSumsSqsubsetCoverageDirByLocationtestPhenotype

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfastmapfilelockfilematrixforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesglmnetgluehmshttrhttr2IRangesiteratorsjsonliteKEGGRESTKernSmoothlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRcppRcppEigenRhtslibrlangRsamtoolsRSQLiteS4ArraysS4VectorsSeqinfoshapesnowSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectutf8vctrswithrxml2XVector

Readme and manuals

Help Manual

Help pageTopics
Fast Methylome-wide Association Study Pipeline for Enrichment Platformsramwas-package ramwas
Cached Loading of RDS FilescachedRDSload
Quickly Find N Smallest P-values in a Long VectorfindBestNpvs
Functions for Access to Data, MWAS Results, and Location InformationgetDataByLocation getLocations getMWAS getMWASandLocations getMWASrange
Construct CpG set for a Reference GenomegetCpGsetALL getCpGsetCG
Inject SNPs from VCF Count File into a DNA SequenceinjectSNPsMAF
Construct FASTQ File for In-silico Alignment ExperimentinsilicoFASTQ
Check if Path is Absolute.isAbsolutePath
Export MWAS results in BED format.madeBED madeBEDgraph madeBEDgraphRange madeBEDrange
Combine Path and Filename into Filename with Pathmakefullpath
Fast Manhattan plot for Large Number of P-valuesmanPlotFast manPlotPrepare
Split a Matrix into Column Vectorsmat2cols
Orthonormalize CovariatesorthonormalizeCovariates
Save Parameters in a Text FileparameterDump
Preprocess Pipeline Parameter List.parameterPreprocess
Scan Parameters From a R Code FileparametersFromFile
RaMWAS: High Level Pipeline Functionspipeline pipelineProcessBam ramwas1scanBams ramwas2collectqc ramwas3normalizedCoverage ramwas4PCA ramwas5MWAS ramwas6annotateTopFindings ramwas7ArunMWASes ramwas7BrunElasticNet ramwas7CplotByNCpGs ramwas7riskScoreCV ramwasSNPs
Plotting Functions used in Cross Validation Analysis (Methylation Risk Score).plotCVcors plotPrediction plotROC
Estimate and plot Fragment Size Distribution.estimateFragmentSizeDistribution plotFragmentSizeDistributionEstimate
Plot Principal component (PC) Values (variation explained) and PC vectors (loadings)plotPCvalues plotPCvectors
Scan Parameters From Command LineprocessCommandLine
Calculate Benjamini-Hochberg q-valuespvalue2qvalue
Quality Control Measuresplot.qcCoverageByDensity plot.qcEditDist plot.qcEditDistBF plot.qcHistScore plot.qcHistScoreBF plot.qcIsoDist plot.qcLengthMatched plot.qcLengthMatchedBF qcmean qcmean.NULL qcmean.qcChrX qcmean.qcChrY qcmean.qcCoverageByDensity qcmean.qcEditDist qcmean.qcEditDistBF qcmean.qcFrwrev qcmean.qcHistScore qcmean.qcHistScoreBF qcmean.qcIsoDist qcmean.qcLengthMatched qcmean.qcLengthMatchedBF qcmean.qcNonCpGreads
Fast QQ-plot for Large Number of P-valuesqqPlotFast qqPlotPrepare
Create Artificial Data Setramwas0createArtificialData
Extract Biomart Annotation for a Vector of Locations.ramwasAnnotateLocations
Function for Convenient Filling of the RaMWAS Parameter List.ramwasParameters
Form Row and Column Sums of SquarescolSumsSq rowSumsSq
Class for Accessing Data (Coverage) MatrixrwDataClass rwDataClass-class
Subset a data matrix and locationssubsetCoverageDirByLocation
Test the Phenotype of Interest for Association with Methylation Coverage.testPhenotype