Files in ijcBIT/cnv.methyl
cnv.methyl finds copy number alteration from methylation idat files
.Rbuildignore
.github/.gitignore
.gitignore
DESCRIPTION
Data/Additional.File.2_TableS1.csv
Data/Additional.File.4_TableS3.csv
Data/CNV_Germline_GSITIC2_BROAD_SNP6.merged.151117.hg19.CNV.txt
Data/CancerGenes.csv
Data/CancerGenes.rds
Data/Custom_Functions.R
Data/S7.csv
Data/S8.xlsx
Data/Sample_Sheet_CL.txt
Data/Table_S1.txt
Data/Table_S2.txt
Data/randomization_sample_sheet.txt
Data/updated_CUP_genes_cnstate.xlsx
LICENSE
LICENSE.md
Manual.Rmd
NAMESPACE
R/DMPextr.R
R/Kc_get.R
R/Kc_make.R
R/TrainingSet_Sample_sheet.R
R/all_CN_ASCAT.R
R/cnv.methyl-package.R
R/pre_process.R
R/run_cnv.methyl.R
R/run_conumee.R
R/sysdata.rda
R/utils.R
README.Rmd
README.md
bin/CL.R
bin/CUPs.R
bin/Randomization.R
bin/Supplementary_table_S8.R
bin/WB_validation.R
bin/functions.R
bin/missing_functions.R
cnv.methyl.Rproj
data-raw/.gitignore
data-raw/AllSamples_SS_raw.R
data-raw/DATASET.R
data-raw/TrainingSet_Sample_sheet.R
data-raw/Training_samples.txt
data-raw/WB_controls.R
data-raw/all_CN_ASCAT.R
data-raw/anno.R
data-raw/anno.rds
data-raw/anno_450K.R
data-raw/anno_overlap.R
data-raw/genes_coords.R
data-raw/sysdata.R
data/AllGenes.rda
data/AllSamples_SS_raw.rda
data/CancerGenes.rda
data/TrainingSet_Sample_sheet.rda
data/all_CN_ASCAT.rda
data/anno_overlap.rda
data/beta_noob.rds
data/cols.rda
data/ss.rda
docs/404.html
docs/LICENSE-text.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/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/SCNA-package.html
docs/reference/index.html
docs/sitemap.xml
inst/CITATION
inst/extdata/Sample_sheet_example.csv
inst/extdata/intensities.RDS
inst/extdata/sample_IDATS/6004791006_R04C02_Grn.idat
inst/extdata/sample_IDATS/6004791006_R04C02_Red.idat
inst/extdata/sample_IDATS/6004791006_R06C02_Grn.idat
inst/extdata/sample_IDATS/6004791006_R06C02_Red.idat
inst/extdata/sample_IDATS/6004791010_R02C02_Grn.idat
inst/extdata/sample_IDATS/6004791010_R02C02_Red.idat
inst/extdata/sample_IDATS/6004791020_R02C02_Grn.idat
inst/extdata/sample_IDATS/6004791020_R02C02_Red.idat
inst/extdata/sample_IDATS/6026818055_R03C02_Grn.idat
inst/extdata/sample_IDATS/6026818055_R03C02_Red.idat
inst/extdata/sample_IDATS/6026818102_R01C01_Grn.idat
inst/extdata/sample_IDATS/6026818102_R01C01_Red.idat
inst/extdata/sample_IDATS/6264488074_R02C02_Grn.idat
inst/extdata/sample_IDATS/6264488074_R02C02_Red.idat
inst/extdata/sample_IDATS/6285633054_R05C01_Grn.idat
inst/extdata/sample_IDATS/6285633054_R05C01_Red.idat
inst/extdata/sample_IDATS/6929742041_R03C02_Grn.idat
inst/extdata/sample_IDATS/6929742041_R03C02_Red.idat
inst/extdata/sample_IDATS/7786923075_R01C01_Grn.idat
inst/extdata/sample_IDATS/7786923075_R01C01_Red.idat
inst/extdata/sample_IDATS/8784241020_R05C02_Grn.idat
inst/extdata/sample_IDATS/8784241020_R05C02_Red.idat
inst/extdata/sample_IDATS/8784241076_R04C01_Grn.idat
inst/extdata/sample_IDATS/8784241076_R04C01_Red.idat
inst/extdata/sample_IDATS/8784241132_R02C01_Grn.idat
inst/extdata/sample_IDATS/8784241132_R02C01_Red.idat
inst/extdata/sample_IDATS/9283265144_R04C02_Grn.idat
inst/extdata/sample_IDATS/9283265144_R04C02_Red.idat
inst/extdata/sample_IDATS/9283265144_R06C01_Grn.idat
inst/extdata/sample_IDATS/9283265144_R06C01_Red.idat
inst/extdata/sample_IDATS/9305216074_R05C01_Grn.idat
inst/extdata/sample_IDATS/9305216074_R05C01_Red.idat
inst/extdata/sample_IDATS/9305216074_R05C02_Grn.idat
inst/extdata/sample_IDATS/9305216074_R05C02_Red.idat
inst/extdata/sample_IDATS/9305216121_R02C01_Grn.idat
inst/extdata/sample_IDATS/9305216121_R02C01_Red.idat
inst/extdata/sample_IDATS/9305216121_R06C01_Grn.idat
inst/extdata/sample_IDATS/9305216121_R06C01_Red.idat
inst/extdata/sample_IDATS/9305216126_R03C02_Grn.idat
inst/extdata/sample_IDATS/9305216126_R03C02_Red.idat
man/DMPextr.Rd
man/Kc_get.Rd
man/Kc_make.Rd
man/TrainingSet_Sample_sheet.Rd
man/cnv.methyl-package.Rd
man/figures/README-pressure-1.png
man/pre_process.Rd
man/read.metharray.exp.par.Rd
man/run_cnv.methyl.Rd
man/run_conumee.Rd
man/scna.Rd
references.bib
tests/testthat.R
tests/testthat/test-concat_two_vec.R
tests/testthat/test-purify.R
todo
