b49c2aa26f0d9a6a38b9eaeb998ee628 *DESCRIPTION
bc8a8ab03cc2bbd76c79e46712e36b4d *NAMESPACE
d9b905c846ab5c274560950599c62fd1 *R/QPforSig.R
1eb1fa8ac622106ff9e97630824c4cb7 *R/addBestSignatureToSubset.R
1629d98fe572f8f89767103a48af7b8f *R/adjustSignaturesForRegionSet.R
f8f7398f7a282612b8f7fa3a554f0afd *R/buildGenomesFromMutationData.R
69ab62e0eac0b083d5bcc8c3b94750e4 *R/buildSortedAlexandrovSignaturePatternList.R
c9706754b9e55a6d4596053d5038f371 *R/composeGenomesFromExposures.R
491a713e50f354159ccf71be8bce3e6d *R/computeExplainedVariance.R
acc807a7f96bc5a4ded5802b3fd46cbf *R/convAlx2Shi.R
47900e3adfd36239fefde3afeb5ebbd2 *R/convertAlexandrov2Shiraishi.R
bb6cfd803bc02f11f536502aff7a65fe *R/convertGenomesFromVRanges.R
1ad9410dc99c8f07d7c1121a4824cb5a *R/convertMutTypesFromAlexandrov_v3_5.R
474e3087f2b65bc986fb3b74a2c393a0 *R/decompTumor2Sig-package.R
5e6f335b129506b6691c54cbeecf0ada *R/decomposeTumorGenomes.R
584e74ed42249dba65efa8cff9723c9b *R/determineSignatureDistances.R
47c405ff6531567e4c9439d0f788fb40 *R/determineTypeNumBasesAndTrDir.R
b448fa7dcf454bf86a3bc9addda17887 *R/downgradeShiraishiSignatures.R
36781185331ddacd9f82831777717655 *R/evaluateDecompositionQuality.R
ea6798769853eb8dfad9add686aebcd6 *R/external_classes_wrapper_functions.R
f1d4fdb22974c8791e7afd08b60d9228 *R/getBestDecomp4Ksignatures.R
bd55f33b94c8b2b38f6f7b7b2e2ac687 *R/getGenomesFromMutFeatData.R
da9a0bd65efafb10439a8bc673b31ddb *R/getSignaturesFromEstParam.R
b37d0c54af886ed07eb3826df2c1874b *R/helper_functions_for_class_checks.R
fd55048925dc8e6cd68e5bb4774046f3 *R/helper_functions_for_sequences.R
50cce7a81f91f83a50feda46a81fcf04 *R/mapSignatureSets.R
886a863010cc10580873de936ef8eb14 *R/mathematical_functions.R
1f30ae4ed82132620655c204ce17dd7f *R/onAttach.R
9a61c5ba4db01a38d9cd8a1dc652de93 *R/plotAlexandrovModel.R
dea0a7d083f646c6a9e4fe8627785127 *R/plotDecomposedContribution.R
26deb33f10e188e7924e292d71ba1204 *R/plotExplainedVariance.R
d41d8b81e7730e3e23b9e92db54c3ef1 *R/plotMutationDistribution.R
69e8d75b3107f29ad44987e85e5b0d06 *R/plotShiraishiModel.R
2809646c205bc2e7f1855748c281d5b1 *R/processMultipleSigSets.R
d1f339e4bb8da8b0d674cdc9e743e3e8 *R/readAlexandrovSignatures.R
97b1eaddd2f75517194d3fbf6847f2bb *R/readGenomesFromMPF.R
2428a3861b0b8bc3377c15e3d897efd3 *R/readGenomesFromVCF.R
7842422438c61564542003e30d03b022 *R/readShiraishiSignatures.R
067047ae1757ea5deb429cac1ca9b6ac *R/setNames4ShiraishiTable.R
8a16254a4caae46bdebb981fc049e97d *README.md
f79b01406f2707e7899e0768c188a08c *build/vignette.rds
b3e92d70d39b7892ead0ba494a3f82a6 *decompTumor2Sig-manual.pdf
770d52bdb5b9d73162c507d905ef1fe4 *inst/CITATION
f75f9fb81a343cca58098b2e4398b119 *inst/NEWS
cfadd070b6bcaf2e81b5ec7c41c85965 *inst/doc/decompTumor2Sig.R
adc42d4f460308ae57050b3b00cf1310 *inst/doc/decompTumor2Sig.Rmd
0a6e1d47bb03c941bbf73fb41d8f42c2 *inst/doc/decompTumor2Sig.html
71d5489dca9fd1d3e22149041f3cbcc4 *inst/extdata/Alexandrov_PMID_23945592_435_tumors-pmsignature-15sig.Rdata
3f0cacddf1a60c7705c8beab9a2eea90 *inst/extdata/Nik-Zainal_PMID_22608084-MPF-hg38.txt.gz
c9dc27bb88c4c9d4ff00036ddb81612f *inst/extdata/Nik-Zainal_PMID_22608084-genomes-Alexandrov_3bases.Rdata
ba1243de9778074a4bdc87df3ff9cb72 *inst/extdata/Nik-Zainal_PMID_22608084-genomes-Shiraishi_5bases_trDir.Rdata
782e9c0a35fd36b2c3d8b53f026dca98 *inst/extdata/Nik-Zainal_PMID_22608084-hg38.vcf.gz
c480ff0e92617ec448e63f777069f090 *inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-G.Rdata
7c851f642f63a00f130030e809cedbba *inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-Param.Rdata
82e7fdbf5a07f0d177a15fbd6701a552 *inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sig1.tsv
678103097909f0de0b36a18e4f49934c *inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sig2.tsv
5f3777474c68d244c72de1c90b0a908c *inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sig3.tsv
2efa22bf8e8537eef40782727527991e *inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sig4.tsv
1536fc34c7646771e45602d6a2ddf007 *inst/extdata/Nik-Zainal_PMID_22608084-pmsignature-sigall.Rdata
94d55d512a9ba36caa9b7df079bae19f *inst/license/COPYING
9f94f627b12210584ac8cbd72cff5bb3 *inst/script/Alexandrov_PMID_23945592_435_tumors-pmsignature-15sig.R
473e4429eb28bbfd5a94a32813608b7a *inst/script/Alexandrov_PMID_23945592_435_tumors-pmsignature-15sig.sh
4b00a42bacf4cff0bced438e3ded178e *inst/script/Nik-Zainal_PMID_22608084-MPF.txt.gz.sh
efc64eb7c925bdf906d0123fab898fa1 *inst/script/Nik-Zainal_PMID_22608084-VCF-convertedfromMPF.vcf.gz.sh
734a9b2fcb18b5a07367be0d1cfdba9c *inst/script/Nik-Zainal_PMID_22608084-genomes.R
1603815dc5e22bf34583383bb25bf780 *inst/script/Nik-Zainal_PMID_22608084-pmsignature.R
8fc6b096fe82526c694c664857864d23 *inst/script/extractSpecColumns.pl
9b1a13dcbf342106de8b08ab7ee518a7 *inst/script/filterLines.pl
69df8e2387e5f27e710e4233f849cc4b *inst/script/filterLinesNumeric.pl
f6fc8f98bcba7ef3b984d20e231a5b2b *man/QPforSig.Rd
f672f264007e314790628238570511d4 *man/addBestSignatureToSubset.Rd
1c9b0333b6ae6c7016b22c6d68bc8868 *man/adjustAlexandrovSignature.Rd
e1cfe4387a1b63acfa745212b1a0666c *man/adjustShiraishiSignature.Rd
27a0701e707ce924df8d280f6e80b448 *man/adjustSignaturesForRegionSet.Rd
9a71e646f6d7f7aea6a83ef67cc513f9 *man/buildGenomesFromMutationData.Rd
eb57207b00cde12b2b180bd1d324d6e9 *man/buildSortedAlexandrovSignaturePatternList.Rd
8d0d036bb2efc368233f5e79ab47cd4b *man/compNucFreq.Rd
b034fd222b9cdf2d9b6b18473fffe60c *man/composeGenomesFromExposures.Rd
ea80ca0082c3def7ba04a16676d4e817 *man/computeExplainedVariance.Rd
b11198ae86b0998ab82013b159fade12 *man/computeFrobeniusNorm.Rd
b8917bd9e09abe54fb6576e3ee63f715 *man/computeRSS.Rd
8f79b0a1160a531ec42171f9a426870e *man/convAlx2Shi.Rd
c6cc17e52eb8bd2d7f51aa6a25d22d3f *man/convertAlexandrov2Shiraishi.Rd
8b4ecaec7c0f34340f8dd23d3c3c03be *man/convertGenomesFromVRanges.Rd
cc4628c6f44dc79c40c46997c76f6148 *man/convertMutTypesFromAlexandrov_v3_5.Rd
c6d0582500a94d54aeb8091eff2839fd *man/convertSeqFreqToBaseFreq.Rd
44bb882d0333c92aa5de082357078f7e *man/decompTumor2Sig-package.Rd
7af2243f13ab8febc5f7d15bbf567ce6 *man/decomposeTumorGenomes.Rd
a6357d601cb5f26f32c3eb77f9d0bc1f *man/determineSignatureDistances.Rd
170f0133011724068425b8d84ce62d93 *man/determineTypeNumBasesAndTrDir.Rd
79a834731ffefeb2933493a9a3038029 *man/downgradeShiraishiSignatures.Rd
0fb9eb55d83f76a91655e1e78432a35e *man/evaluateDecompositionQuality.Rd
effb2baf850c909fc4116f835ece0652 *man/getBestDecomp4Ksignatures.Rd
35faf8c3c553cabe3694a8fd1e2cb01d *man/getCountData.Rd
b03a231a018503cc6c984d0a3fb71efb *man/getFeatVectList.Rd
c82862627b800054ed394cde4bd2f9c0 *man/getGenomesFromMutFeatData.Rd
ee6c10f27eb3a6091bff96ad280e57f2 *man/getNumFlankingBases.Rd
d267fb099a14a1cf69cabb82820dca08 *man/getNumSignatures.Rd
b945a756ddabf3041a99f81434b3e2f2 *man/getSampleList.Rd
6aeb8c15a1df26a541ea9694538fe3d0 *man/getSigFeatDist.Rd
01421905d56b452ba6eada5850dd31de *man/getSigFromEstParam.Rd
2595170e5a63c1be4a04a864fd82d689 *man/getSigType.Rd
5f3584c0f933d97a3d399a22f74c0e16 *man/getSignaturesFromEstParam.Rd
296829d526b36baacf85d0e14fb8cd3c *man/haveTrDir.Rd
48badce9e7d8cb77f3452c2446e26230 *man/is.probability.data.frame.Rd
5f7e8ba33974836e2eead5bacfd58505 *man/is.probability.data.frame.list.Rd
15632e4829a3e8681eabfd0eae1e1f92 *man/is.probability.matrix.Rd
1b699c9bf154811f177c8ea898d2871e *man/is.probability.matrix.list.Rd
bee70e56c9c1afa9845247f4cb63b170 *man/is.probability.object.Rd
f47cc356a3cd1cd75d63861cc3c2e4e8 *man/is.probability.vector.Rd
2a043265377c0aa27f1585c6e6dff7e7 *man/is.probability.vector.list.Rd
7db4a8787cc814cadb523bcef532f7f7 *man/isAlexandrovSet.Rd
e2e276593f5b8d1ce289138364a38d7a *man/isBackGround.Rd
8434ac956cfa74dcd303e15ff21cae6c *man/isEstParamObject.Rd
dda7f031788347d6dd85d2a5ec2e8940 *man/isExposureSet.Rd
75a095cf1ba9b5e6d05491c97819b796 *man/isMutFeatDataObject.Rd
5bc20a7a221e58ef97bd33105449b7bf *man/isShiraishiSet.Rd
38524af772c623ab7590eaeff425e593 *man/isSignatureSet.Rd
902f576ad9dc43742d64088f8b6d7404 *man/mapSignatureSets.Rd
19ad433381f11716595dc4bf9638875b *man/plotAlexandrovModel.Rd
df1a0338e259f8009a2af3053e340c0f *man/plotDecomposedContribution.Rd
ab4a9bd6f1adff8172d3a1382525e439 *man/plotExplainedVariance.Rd
7bb0ba5e550de3dd97858249f4f260f2 *man/plotMutationDistribution.Rd
7f5e43708c1f64aa457271a904a485c3 *man/plotShiraishiModel.Rd
16f3057bbc25572bb1268a3247505bc0 *man/processMultipleSigSets.Rd
03ab18e19c438a2e244c5550a29d0e3b *man/readAlexandrovSignatures.Rd
b4e152393df9f95bbb209599a491059c *man/readGenomesFromMPF.Rd
5a94d25a870b40b7de3e06e33417fb4f *man/readGenomesFromVCF.Rd
ebe0ba24198db6cae5da9ab35f0b753e *man/readShiraishiSignatures.Rd
5a7750e977c6344efa84f1e1a371d05d *man/roundIntegerSum.Rd
c2a73c3912b7077ca18aae1cc96f2ae0 *man/sameSignatureFormat.Rd
1f3cb2006620b6a18d28a64575b728d0 *man/setNames4ShiraishiTable.Rd
36812bd7c01acf4880c6a7a753fce24e *man/setNumFlankingBases.Rd
5758d95ab5f40658211528e15226e954 *man/setSigFeatDist.Rd
5f6e2141a4b4a87632f2751f9a708bf2 *man/setSigType.Rd
e4bc6f3362e7b67aeab38e79f429a81e *man/setTrDir.Rd
adc42d4f460308ae57050b3b00cf1310 *vignettes/decompTumor2Sig.Rmd
80b89b0a22426bb979abeb75b50afa4e *vignettes/example-sign-Shiraishi.png
