Files in belleau/aicsPaper
Accurate Inference of Genetic Ancestry from Cancer Sequencing
.github/.gitignore
.github/workflows/check-bioc.yaml
.github/workflows/test-coverage.yaml
DESCRIPTION
LICENSE
NAMESPACE
R/aicsPaper.R
R/allelicFraction.R
R/gdsWrapper.R
R/process1KG.R
R/processStudy.R
R/synthetic.R
R/tools.R
README.md
aicsPaper_project.Rproj
doc/README_1KG_GDS.md
doc/README_GDS.struct.md
doc/README_StudyInit.md
inst/extdata/1KG_Demo.gds
inst/extdata/HG00100.csv.bz2
inst/extdata/HG00101.csv.bz2
inst/extdata/HG00102.csv.bz2
inst/extdata/HG00103.csv.bz2
inst/extdata/HG00104.csv.bz2
inst/extdata/HG00105.csv.bz2
inst/extdata/HG00106.csv.bz2
inst/extdata/HG00107.csv.bz2
inst/extdata/HG00108.csv.bz2
inst/extdata/HG00109.csv.bz2
inst/extdata/PedigreeDemo.ped
inst/extdata/PedigreeDemo.rds
inst/extdata/listSNPIndexes_Demo.rds
inst/extdata/mapSNVSelected_Demo.rds
inst/extdata/matFreqSNV_Demo.txt.bz2
inst/extdata/tests/1KG_Test.gds
inst/extdata/unrelatedPatientsInfo_Demo.rds
man/RAIDS-package.Rd
man/add1KG2SampleGDS.Rd
man/addBlockFromPlink2GDS.Rd
man/addGDS1KGLDBlock.Rd
man/addGDSRef.Rd
man/addGDSStudyPruning.Rd
man/addPhase1KG2SampleGDSFromFile.Rd
man/addPhase1KG2SampleGDSFromGDS.Rd
man/addRef2GDS1KG.Rd
man/addStudy1Kg.Rd
man/addStudyGDSSample.Rd
man/addUpdateLap.Rd
man/addUpdateSegment.Rd
man/appendGDSSample.Rd
man/appendGDSSampleOnly.Rd
man/appendGDSgenotype.Rd
man/appendGDSgenotypeMat.Rd
man/appendStudy2GDS1KG.Rd
man/basePCASample.Rd
man/computeAlleleFraction.Rd
man/computeAllelicFractionDNA.Rd
man/computeAllelicImbDNAChr.Rd
man/computeKNNSuperPoprSynthetic.Rd
man/computeLOHBlocksDNAChr.Rd
man/computePCAForSamples.Rd
man/computePCAsynthetic.Rd
man/computePrunedPCARef.Rd
man/computeSyntheticConfMat.Rd
man/computeSyntheticROC.Rd
man/estimateAllelicFraction.Rd
man/gds2tfam.Rd
man/gds2tfamSample.Rd
man/gds2tped.Rd
man/generateGDS1KG.Rd
man/generateGDS1KGgenotypeFromSNPPileup.Rd
man/generateGDSSNPinfo.Rd
man/generateGDSSample.Rd
man/generateGDSgenotype.Rd
man/generateMapSnvSel.Rd
man/generatePhase1KG2GDS.Rd
man/getTableSNV.Rd
man/groupChr1KGSNV.Rd
man/groupChrPruning.Rd
man/identifyRelative.Rd
man/prepPed1KG.Rd
man/prepPedSynthetic1KG.Rd
man/prepSynthetic.Rd
man/processBlockChr.Rd
man/projectSample2PCA.Rd
man/pruning1KG.Chr.Rd
man/pruningSample.Rd
man/runIBDKING.Rd
man/runLDPruning.Rd
man/selParaPCAUpQuartile.Rd
man/select1KGPop.Rd
man/snvListVCF.Rd
man/syntheticGeno.Rd
man/testAlleleFractionChange.Rd
man/testEmptyBox.Rd
scriptsPy/extract1000gFreqAll.py
tests/testthat.R
tests/testthat/test-allelicFraction.R
tests/testthat/test-process1KG.R
tests/testthat/test-processStudy.R
tests/testthat/test-synthetic.R
tests/testthat/test-tools.R
vignettes/MainSteps_Step1_v01.png
vignettes/MainSteps_Step2_v01.png
vignettes/MainSteps_v01.png
vignettes/aicsBiblio.bibtex
vignettes/aicsPaper.Rmd
vignettes/groupChr1KGSNV_v01.png
