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ACAT()
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Combine P-values using the ACAT method. |
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aggregate(<gdb>)
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Aggregate genotypes into a single (burden) score for each individual |
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aggregateFile listSamples getUnit aggregateFile-class show,aggregateFile-method listUnits,aggregateFile-method listSamples,aggregateFile-method metadata,aggregateFile-method getGdbId,aggregateFile-method getRvatVersion,aggregateFile-method getUnit,aggregateFile-method
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Class to manage interactions with an aggregateFile |
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aggregateFileList aggregateFileList-class show,aggregateFileList-method listUnits,aggregateFileList-method listSamples,aggregateFileList-method length,aggregateFileList-method metadata,aggregateFileList-method
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Class to facilitate merging aggregateFiles |
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assocTest(<aggregateFile>)
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assocTest-aggregateFile |
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assocTest(<gdb>)
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assocTest-gdb |
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assocTest(<genoMatrix>)
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assocTest-genoMatrix |
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assocTest
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Perform association tests on binary or quantitative traits |
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buildCorMatrix()
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buildCorMatrix |
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buildGdb()
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Create a gdb file. |
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buildGeneSet()
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Build a geneSetList or geneSetFile |
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buildResamplingFile()
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Build a resampling matrix |
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buildVarSet(<data.frame>)
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buildVarSet-data.frame |
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buildVarSet(<gdb>)
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buildVarSet-gdb |
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buildVarSet
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buildVarSet |
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collapseAggregateFiles()
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Collapse multiple aggregate files |
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concatGdb()
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Concatenate gdb databases |
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densityPlot()
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Density plot |
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dropTable()
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Drop table from gdb |
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%$%
|
Exposition pipe |
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extractRanges()
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Extract variants from a gdb based on a set of ranges |
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fitNullModelGSA()
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fitNullModelGSA |
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forestplot()
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forestplot Makes a forest plot of the effect size of all occurrences of the chosen gene set |
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gdb listAnno listCohort getRvatVersion getGdbId getGdbPath getGenomeBuild getCreationDate gdb-class show,gdb-method close,gdb-method listAnno,gdb-method listCohort,gdb-method getRvatVersion,gdb-method getGdbId,gdb-method getGdbPath,gdb-method getCreationDate,gdb-method getGenomeBuild,gdb-method dropTable,gdb-method
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Connect and interact with a gdb |
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geneSet geneSet-class metadata,geneSet-method length,geneSet-method as.data.frame,geneSet-method listUnits,geneSet-method listWeights,geneSet-method
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Class that represents a geneSet |
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geneSetAssoc()
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geneSetAssoc |
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geneSetFile()
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Class to manage interactions with a geneSetFile |
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geneSetList listMetadata dropUnits remapIDs geneSetList-class names,geneSetList-method length,geneSetList-method lengths,geneSetList-method show,geneSetList-method metadata,geneSetList-method listMetadata,geneSetList-method listGeneSets,geneSetList-method listUnits,geneSetList-method [[,geneSetList,ANY,missing-method [,geneSetList,ANY,ANY,ANY-method sort,geneSetList-method as.data.frame,geneSetList-method as.list,geneSetList-method dropUnits,geneSetList-method remapIDs,geneSetList-method write,geneSetList-method
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Class to manage multiple geneSets |
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genoMatrix getAF getMAF getAC getMAC getNCarriers getCR updateGT flipToMinor getCarriers genoMatrix-class show,genoMatrix-method getAF,genoMatrix-method getMAF,genoMatrix-method getAC,genoMatrix-method getMAC,genoMatrix-method getNCarriers,genoMatrix-method getCR,genoMatrix-method summariseGeno,genoMatrix-method [,genoMatrix,ANY,ANY,ANY-method updateGT,genoMatrix-method flipToMinor,genoMatrix-method recode,genoMatrix-method aggregate,genoMatrix-method getCarriers,genoMatrix-method
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The genoMatrix class for storing genotype data and associated sample and variant info. |
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getAnno()
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Get an annotation table from a gdb |
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getCohort()
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Get an cohort table from a gdb |
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getGT()
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Load genotypes from a gdb. |
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getGeneSet()
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Get geneset(s) from a geneSetList/geneSetFile |
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getRanges()
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getRanges |
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getVarSet()
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Retrieve varSet records from a varSetFile or varSetList |
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gsaResult()
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Create a gsaResult-class |
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listGeneSets()
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Return names of geneSets included in a geneSetFile or geneSetList |
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listUnits()
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Return the units included in an varSetFile/varSetList/aggregateFile |
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listVarSets()
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Return names of varsets included in a varSetFile or varSetList |
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listWeights()
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Return names of weights included in a varSet or geneSet |
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manhattan()
|
Generate manhattan plot |
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mapToCDS()
|
mapToCDS |
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mapVariants()
|
mapVariants |
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mergeAggregateFiles()
|
Merge multiple aggregate files |
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mutationPlot()
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Mutation Plot |
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listUnits(<nullModelGSA>) length(<nullModelGSA>) show(<nullModelGSA>)
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An S4 class to store and handle null models for mixed linear model gene set analysis. |
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%>%
|
Pipe |
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qqplot()
|
Generate a qq-plot |
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readGMT()
|
Read a gmt-file |
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readResults()
|
Read association results |
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recode()
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Recode genotypes |
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resamplingFile resamplingFile-class show,resamplingFile-method
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Generate and manage permutations |
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rvatResult topResult rvatResult-class rvbResult-class singlevarResult-class gsaResult-class writeResult,rvatResult-method getGdbId,rvatResult-method getGenomeBuild,rvatResult-method merge,rvatResult,data.frame-method merge,rvatResult,DataFrame-method topResult,rvatResult-method qqplot,rvatResult-method manhattan,rvatResult-method rvbResult summary,rvbResult-method ACAT,rvatResult-method singlevarResult summary,singlevarResult-method summary,gsaResult-method
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Class for handling and visualizing results generated using rvat. |
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rvatViewer()
|
rvatViewer |
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spatialClust()
|
Generate variant sets based on spatial clustering |
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subsetGdb()
|
Generate subset of gdb, retaining all tables. |
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summariseGeno(<gdb>)
|
Return variant summaries |
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uploadAnno()
|
Upload variant annotation into gdb. |
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uploadCohort()
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Upload cohort table into gdb. |
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varSet listVars varSet-class mapToCDS,gdb-method show,varSet-method metadata,varSet-method getGdbId,varSet-method getRvatVersion,varSet-method listVars,varSet-method listWeights,varSet-method as.data.frame,varSet-method
|
Class that represents a set of variants and weights |
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varSetFile varSetFile-class show,varSetFile-method metadata,varSetFile-method getGdbId,varSetFile-method getRvatVersion,varSetFile-method length,varSetFile-method listUnits,varSetFile-method listVarSets,varSetFile-method getVarSet,varSetFile-method
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Class to manage interactions with a varSetFile |
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varSetList collapseVarSetList varSetList-class show,varSetList-method length,varSetList-method [[,varSetList,ANY,missing-method [,varSetList,ANY,ANY,ANY-method listUnits,varSetList-method listVarSets,varSetList-method getGdbId,varSetList-method getRvatVersion,varSetList-method getVarSet,varSetList-method write,varSetList-method as.data.frame,varSetList-method collapseVarSetList,varSetList-method metadata,varSetList-method
|
Class to manage multiple varSets |
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vcfInfo2Table()
|
Convert vcf info field to table format |
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writeResult()
|
Write an rvatResult to disk. |
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writeVcf()
|
writeVcf |