Files in lculibrk/Ploidetect-package
Interpretable detection of tumour purity, ploidy, copy number variation and loss of heterozygosity
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/Ploidetect.R
R/Ploidetect_refineCNAs.R
R/callbreakponts.R
R/centromeres_doc.R
R/compressdata.R
R/lineartransform.R
R/merge_mafs.R
R/modelbuilder_iterative.R
R/optimizesmoothing.R
R/peakcaller.R
R/ploidetect_filter_xdists.R
R/ploidetect_loh.R
R/ploidetect_preprocess.R
R/ploidetect_processallpeaks.R
R/ploidetect_roughmodels.R
R/ploidetect_segmentator.R
R/ploidetect_transform.R
R/read_ploidetect.R
R/runiterativecompression.R
R/softmax.R
R/sumexp.R
R/testmaf.R
README.md
data/centromeres.RData
demo/Demo.Rmd
demo/Demo.md
demo/Demo_files/figure-html/pressure-1.png
demo/Demo_files/figure-html/pressure-2.png
demo/Demo_files/figure-html/pressure-3.png
demo/Demo_files/figure-html/pressure-4.png
demo/Demo_files/figure-html/pressure-5.png
demo/Demo_files/figure-html/pressure-6.png
demo/Demo_files/figure-html/pressure-7.png
demo/Demo_files/figure-html/unnamed-chunk-11-1.png
demo/Demo_files/figure-html/unnamed-chunk-2-1.png
demo/Demo_files/figure-html/unnamed-chunk-2-2.png
demo/Demo_files/figure-html/unnamed-chunk-3-1.png
demo/Demo_files/figure-html/unnamed-chunk-3-10.png
demo/Demo_files/figure-html/unnamed-chunk-3-11.png
demo/Demo_files/figure-html/unnamed-chunk-3-12.png
demo/Demo_files/figure-html/unnamed-chunk-3-13.png
demo/Demo_files/figure-html/unnamed-chunk-3-14.png
demo/Demo_files/figure-html/unnamed-chunk-3-15.png
demo/Demo_files/figure-html/unnamed-chunk-3-16.png
demo/Demo_files/figure-html/unnamed-chunk-3-17.png
demo/Demo_files/figure-html/unnamed-chunk-3-18.png
demo/Demo_files/figure-html/unnamed-chunk-3-19.png
demo/Demo_files/figure-html/unnamed-chunk-3-2.png
demo/Demo_files/figure-html/unnamed-chunk-3-20.png
demo/Demo_files/figure-html/unnamed-chunk-3-3.png
demo/Demo_files/figure-html/unnamed-chunk-3-4.png
demo/Demo_files/figure-html/unnamed-chunk-3-5.png
demo/Demo_files/figure-html/unnamed-chunk-3-6.png
demo/Demo_files/figure-html/unnamed-chunk-3-7.png
demo/Demo_files/figure-html/unnamed-chunk-3-8.png
demo/Demo_files/figure-html/unnamed-chunk-3-9.png
demo/Demo_files/figure-html/unnamed-chunk-4-1.png
demo/Demo_files/figure-html/unnamed-chunk-5-1.png
demo/Demo_files/figure-html/unnamed-chunk-6-1.png
demo/Demo_files/figure-html/unnamed-chunk-7-1.png
demo/Demo_files/figure-html/unnamed-chunk-7-2.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-11-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-17-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-17-2.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-19-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-20-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-21-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-24-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-25-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-26-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-27-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-28-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-29-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-3-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-30-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-31-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-32-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-35-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-35-2.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-36-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-36-2.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-37-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-37-2.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-38-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-4-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-42-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-42-2.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-42-3.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-45-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-5-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-6-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-7-1.png
demo/Demo_files/figure-markdown_github/unnamed-chunk-7-2.png
demo/exampledata.txt
man/ploidetect.Rd
