├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── bam_qc_calc.r ├── bam_qc_plot.r ├── getByLocation.r ├── param.r ├── plotting.r ├── ramwas.r ├── rowcolSumSq.r ├── rw0simdata.r ├── rw1scanBam.r ├── rw2collectqc.r ├── rw3covMatrix.r ├── rw4pca.r ├── rw5mwas.r ├── rw6anno.r ├── rw7mmcv.r ├── rwCellTypeEst.r ├── rwCpGset.r ├── rwDataClass.r ├── rwDataSubset.r └── rwSNPS.r ├── README.md ├── inst ├── CITATION └── extdata │ ├── bigQC.rds │ ├── cpgset.rds │ ├── param_file.txt │ ├── qc_sample.rds │ └── small.bam ├── man ├── MakeBED.Rd ├── QCs.Rd ├── RaMWAS.Rd ├── cachedRDSload.Rd ├── figures │ └── hint.png ├── findBestNpvs.Rd ├── get.Rd ├── getCpGset.Rd ├── injectSNPsMAF.Rd ├── insilicoFASTQ.Rd ├── isAbsolutePath.Rd ├── makefullpath.Rd ├── manhattan.Rd ├── mat2cols.Rd ├── orthonormalizeCovariates.Rd ├── parameterDump.Rd ├── parameterPreprocess.Rd ├── parametersFromFile.Rd ├── pipeline.Rd ├── plotCV.Rd ├── plotFragmentSizeDistributionEstimate.Rd ├── plotPC.Rd ├── processCommandLine.Rd ├── pvalue2qvalue.Rd ├── qqplotFast.Rd ├── ramwas0createArtificialData.Rd ├── ramwasAnnotateLocations.Rd ├── ramwasParameters.Rd ├── rowcolSumSq.Rd ├── rwDataClass-class.Rd ├── subsetData.Rd └── testPhenotype.Rd ├── ramwas.Rproj ├── src └── rw_c_code.c └── vignettes ├── Flow.png ├── PCval.png ├── PCvec.png ├── QQfull.png ├── QQnull.png ├── RW1_intro.Rmd ├── RW2_CpG_sets.Rmd ├── RW3_BAM_QCs.Rmd ├── RW4_SNPs.Rmd ├── RW5a_matrix.Rmd ├── RW5c_matrix.Rmd ├── RW6_param.Rmd └── bib.bib /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andreyshabalin/ramwas/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/andreyshabalin/ramwas/HEAD/.gitignore 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