Files in lima1/PureCN
Copy number calling and SNV classification using targeted short read sequencing

.Rbuildignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/PureCN-internal.R R/annotateTargets.R R/bootstrapResults.R R/calculateBamCoverageByInterval.R R/calculateGCContentByInterval.R R/calculateLogRatio.R R/callAlterations.R R/callLOH.R R/callMutationBurden.R R/correctCoverageBias.R R/createCurationFile.R R/createNormalDatabase.R R/filterTargets.R R/filterVcf.R R/filterVcfMuTect2.R R/findBestNormal.R R/findFocal.R R/getSex.R R/plotAbs.R R/poolCoverage.R R/powerDetectSomatic.R R/predictSomatic.R R/readCoverageFile.R R/readCurationFile.R R/runAbsoluteCN.R R/segmentationCBS.R R/segmentationPSCBS.R R/setMappingBiasVcf.R README.md
data/centromeres.rda
data/purecn.example.output.rda
inst/CITATION
inst/extdata/Coverage.R inst/extdata/Dx.R inst/extdata/FilterCallableLoci.R inst/extdata/IntervalFile.R inst/extdata/NormalDB.R inst/extdata/PureCN.R inst/extdata/downloadCentromeres.R
inst/extdata/ex1.bam
inst/extdata/ex1.bam.bai
inst/extdata/ex1_gcgene.txt
inst/extdata/ex1_intervals.txt
inst/extdata/ex2_intervals.bed
inst/extdata/ex2_intervals.txt
inst/extdata/ex2_mappability.bed
inst/extdata/ex2_mappability.bigWig
inst/extdata/ex2_reference.fa
inst/extdata/ex2_reference.fa.fai
inst/extdata/ex3_intervals.bed
inst/extdata/ex3_mappability.bed
inst/extdata/ex3_reference.fa
inst/extdata/ex3_reference.fa.fai
inst/extdata/example_callable.bed.gz
inst/extdata/example_cosmic.vcf.gz
inst/extdata/example_cosmic.vcf.gz.tbi
inst/extdata/example_gc.gene.file.txt
inst/extdata/example_normal.list
inst/extdata/example_normal.txt
inst/extdata/example_normal2.txt
inst/extdata/example_normal3.cnn
inst/extdata/example_normal4.cnr
inst/extdata/example_seg.txt
inst/extdata/example_tumor.txt
inst/extdata/example_vcf.vcf
inst/extdata/normalpanel.vcf.gz
inst/extdata/normalpanel.vcf.gz.tbi
inst/extdata/test_coverage_overlapping_intervals.txt
inst/unitTests/test_annotateTargets.R inst/unitTests/test_bootstrapResults.R inst/unitTests/test_calculateBamCoverageByInterval.R inst/unitTests/test_calculateGCContentByInterval.R inst/unitTests/test_calculatePowerDetectSomatic.R inst/unitTests/test_callAlterations.R inst/unitTests/test_callAlterationsFromSegmentation.R inst/unitTests/test_callLOH.R inst/unitTests/test_callMutationBurden.R inst/unitTests/test_correctCoverageBias.R inst/unitTests/test_createCurationFile.R inst/unitTests/test_createNormalDatabase.R inst/unitTests/test_filterVcf.R inst/unitTests/test_findFocal.R inst/unitTests/test_getSexFromCoverage.R inst/unitTests/test_getSexFromVcf.R inst/unitTests/test_poolCoverage.R inst/unitTests/test_predictSomatic.R inst/unitTests/test_readCoverageFile.R inst/unitTests/test_runAbsoluteCN.R inst/unitTests/test_setMappingBiasVcf.R inst/unitTests/test_setPriorVcf.R man/PureCN-defunct.Rd man/PureCN-deprecated.Rd man/annotateTargets.Rd man/bootstrapResults.Rd man/calculateBamCoverageByInterval.Rd man/calculateGCContentByInterval.Rd man/calculateLogRatio.Rd man/calculatePowerDetectSomatic.Rd man/callAlterations.Rd man/callAlterationsFromSegmentation.Rd man/callLOH.Rd man/callMutationBurden.Rd man/centromeres.Rd man/correctCoverageBias.Rd man/createCurationFile.Rd man/createNormalDatabase.Rd man/createTargetWeights.Rd man/filterTargets.Rd man/filterVcfBasic.Rd man/filterVcfMuTect.Rd man/filterVcfMuTect2.Rd man/findBestNormal.Rd man/findFocal.Rd man/getSexFromCoverage.Rd man/getSexFromVcf.Rd man/plotAbs.Rd man/plotBestNormal.Rd man/poolCoverage.Rd man/predictSomatic.Rd man/purecn.example.output.Rd man/readCoverageFile.Rd man/readCurationFile.Rd man/runAbsoluteCN.Rd man/segmentationCBS.Rd man/segmentationPSCBS.Rd man/setMappingBiasVcf.Rd man/setPriorVcf.Rd tests/runTests.R
vignettes/PureCN.Rnw
vignettes/PureCN.bib
vignettes/Quick.Rnw
lima1/PureCN documentation built on Nov. 9, 2017, 4:14 p.m.