Files in TransBioInfoLab/coMethDMR
Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
R/AnnotateResults.R
R/CloseBySingleRegion.R
R/CoMethAllRegions.R
R/CoMethSingleRegion.R
R/CpGsInfoAllRegions.R
R/CpGsInfoOneRegion.R
R/CreateOutputDF.R
R/CreateRdrop.R
R/FindComethylatedRegions.R
R/GetCpGsInRegion.R
R/GetResiduals.R
R/MarkComethylatedCpGs.R
R/WriteCloseByAllRegions.R
R/create_all_genomic_array_ranges
R/data_betaMatrixChr22_df.R
R/data_betaMatrix_ex1.R
R/data_betaMatrix_ex2.R
R/data_betaMatrix_ex3.R
R/data_betaMatrix_ex4.R
R/data_pheno_df.R
R/lmmTest.R
R/lmmTestAllRegions.R
R/util1_OrderCpGsByLocation.R
R/util2_NameRegion.R
R/util3_SplitCpGsSubregionsDataFrameToList.R
R/util4_RegionsToRanges.R
R/utils_CreateParallelWorkers.R
R/utils_ImportSesameData.R
R/utils_MarkMissing.R
R/zzz.R
README.md
_pkgdown.yaml
data/betaMatrix_ex1.rda
data/betaMatrix_ex2.rda
data/betaMatrix_ex3.rda
data/betaMatrix_ex4.rda
data/betasChr22_df.rda
data/pheno_df.rda
docs/404.html
docs/articles/index.html
docs/articles/vin1_Introduction_to_coMethDMR_geneBasedPipeline.html
docs/articles/vin1_Introduction_to_coMethDMR_geneBasedPipeline_files/figure-html/unnamed-chunk-5-1.png
docs/articles/vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/AnnotateResults.html
docs/reference/CloseBySingleRegion.html
docs/reference/CoMethAllRegions.html
docs/reference/CoMethSingleRegion.html
docs/reference/CpGsInfoAllRegions.html
docs/reference/CpGsInfoOneRegion.html
docs/reference/CreateOutputDF.html
docs/reference/CreateParallelWorkers.html
docs/reference/CreateRdrop.html
docs/reference/FindComethylatedRegions.html
docs/reference/GetCpGsInRegion.html
docs/reference/GetResiduals.html
docs/reference/ImportSesameData.html
docs/reference/MarkComethylatedCpGs.html
docs/reference/MarkMissing.html
docs/reference/NameRegion.html
docs/reference/OrderCpGsByLocation.html
docs/reference/RegionsToRanges.html
docs/reference/Rplot001.png
docs/reference/SplitCpGDFbyRegion.html
docs/reference/WriteCloseByAllRegions.html
docs/reference/betaMatrix_ex1.html
docs/reference/betaMatrix_ex2.html
docs/reference/betaMatrix_ex3.html
docs/reference/betaMatrix_ex4.html
docs/reference/betasChr22_df.html
docs/reference/coMethDMR_setup.html
docs/reference/index.html
docs/reference/lmmTest.html
docs/reference/lmmTestAllRegions.html
docs/reference/pheno_df.html
docs/sitemap.xml
inst/bug_fixes/.gitignore
inst/bug_fixes/issue6_20210427.R
inst/bug_fixes/issue7_20220121.R
inst/extdata/450k_Gene_3_200.rds
inst/extdata/450k_InterGene_3_200.rds
inst/extdata/CpGislandsChr22_ex.rds
inst/extdata/hg19tohg38.rds
inst/scripts/createList_InterGeneCpGs.R
inst/scripts/createList_geneCpGs.R
inst/scripts/create_chr22exFile.R
man/AnnotateResults.Rd
man/CloseBySingleRegion.Rd
man/CoMethAllRegions.Rd
man/CoMethSingleRegion.Rd
man/CpGsInfoAllRegions.Rd
man/CpGsInfoOneRegion.Rd
man/CreateOutputDF.Rd
man/CreateParallelWorkers.Rd
man/CreateRdrop.Rd
man/FindComethylatedRegions.Rd
man/GetCpGsInRegion.Rd
man/GetResiduals.Rd
man/ImportSesameData.Rd
man/MarkComethylatedCpGs.Rd
man/MarkMissing.Rd
man/NameRegion.Rd
man/OrderCpGsByLocation.Rd
man/RegionsToRanges.Rd
man/SplitCpGDFbyRegion.Rd
man/WriteCloseByAllRegions.Rd
man/betaMatrix_ex1.Rd
man/betaMatrix_ex2.Rd
man/betaMatrix_ex3.Rd
man/betaMatrix_ex4.Rd
man/betasChr22_df.Rd
man/coMethDMR_setup.Rd
man/lmmTest.Rd
man/lmmTestAllRegions.Rd
man/pheno_df.Rd
tests/testthat.R
tests/testthat/test_CoMethAllRegions.R
tests/testthat/test_CpGsInfoAllRegions.R
tests/testthat/test_MarkMissing.R
tests/testthat/test_lmmTest.R
tests/testthat/test_lmmTestAllRegions.R
tests/testthat/test_nameRegion.R
vignettes/vin1_Introduction_to_coMethDMR_geneBasedPipeline.Rmd
vignettes/vin2_BiocParallel_for_coMethDMR_geneBasedPipeline.Rmd
