Files in MPIIComputationalEpigenetics/MAGAR
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/GWAPMap.R
R/MethQTLInput-class.R
R/MethQTLResult-class.R
R/cluster.R
R/compute_methQTL.R
R/correlation_blocks.R
R/data_import.R
R/imputation.R
R/interpretation.R
R/options.R
R/plotting.R
R/utilities.R
README.md
inst/CITATION
inst/NEWS
inst/extdata/MethQTLResult_chr18/MethQTLResult.RData
inst/extdata/MethQTLResult_chr18/anno_geno.RDS
inst/extdata/MethQTLResult_chr18/anno_meth.RDS
inst/extdata/MethQTLResult_chr18/correlation_blocks.RDS
inst/extdata/MethQTLResult_chr18/result_frame.RDS
inst/extdata/Rscript/rscript_chromosome_job.R
inst/extdata/Rscript/rscript_summary.R
inst/extdata/Rscript/simulation/create_simulated_data.R
inst/extdata/Rscript/simulation/validate_correlation_blocks.R
inst/extdata/qtl_options_probes450.json
inst/extdata/qtl_options_probesEPIC.json
inst/extdata/reduced_methQTL/MethQTLInput.RData
inst/extdata/reduced_methQTL/anno_geno.RDS
inst/extdata/reduced_methQTL/anno_meth.RDS
inst/extdata/reduced_methQTL/geno_data.h5
inst/extdata/reduced_methQTL/meth_data.h5
inst/extdata/reduced_methQTL/pheno_data.RDS
inst/extdata/rnbeads_options.xml
inst/unitTests/test_structure.R
man/MethQTLInput-class.Rd
man/MethQTLResult-class.Rd
man/QTL.OPTIONS.Rd
man/computeCorrelationBlocks.Rd
man/doImport.Rd
man/doMethQTL.Rd
man/doMethQTLChromosome.Rd
man/filterPval.Rd
man/getAnno.Rd
man/getCorrelationBlocks.Rd
man/getGeno.Rd
man/getMethData.Rd
man/getOverlapUniverse.Rd
man/getOverlappingQTL.Rd
man/getPheno.Rd
man/getResult.Rd
man/getResultGWASMap.Rd
man/getSamples.Rd
man/getSpecificQTL.Rd
man/imputeMeth.Rd
man/joinMethQTLResult.Rd
man/loadMethQTLInput.Rd
man/loadMethQTLResult.Rd
man/overlapInputs.Rd
man/overlapQTLs.Rd
man/qtlAnnotationEnrichment.Rd
man/qtlBaseSubstitutionEnrichment.Rd
man/qtlDistanceScatterplot.Rd
man/qtlGetOption.Rd
man/qtlJSON2options.Rd
man/qtlManhattanPlot.Rd
man/qtlOptions2JSON.Rd
man/qtlPlotBaseSubstitution.Rd
man/qtlPlotClusterSize.Rd
man/qtlPlotSNPCpGInteraction.Rd
man/qtlSetOption.Rd
man/qtlTFBSMotifEnrichment.Rd
man/qtlUpSetPlotCorBlocks.Rd
man/qtlUpSetPlotTagCpGs.Rd
man/qtlUpsetPlot.Rd
man/qtlVennPlot.Rd
man/saveMethQTLInput.Rd
man/saveMethQTLResult.Rd
tests/runTests.R
vignettes/MAGAR.Rmd
vignettes/biblio.bib
vignettes/rnbeads_options.xml
