22d6721cd6f3484429f566c69034d9a5 *DESCRIPTION
28756c33aadb0dee6e3e6168c5101542 *NAMESPACE
aafcb07a909c4e0c217820c33441b794 *R/QPforSig.R
1eb1fa8ac622106ff9e97630824c4cb7 *R/addBestSignatureToSubset.R
c30222d96f27f7edbf5c9f972e48bbbb *R/adjustSignaturesForRegionSet.R
dec23eef373226f13b95b6b9f7511999 *R/buildGenomesFromMutationData.R
69ab62e0eac0b083d5bcc8c3b94750e4 *R/buildSortedAlexandrovSignaturePatternList.R
a52a6a5517d65de3dda0f25c0fc51f79 *R/composeGenomesFromExposures.R
4b318222e56c3a0f3a121a0fd3ecbae8 *R/computeExplainedVariance.R
acc807a7f96bc5a4ded5802b3fd46cbf *R/convAlx2Shi.R
ff69255344508ed453266b7b246ec93e *R/convertAlexandrov2Shiraishi.R
05b85454e58882dc76cd06aa1cfea165 *R/convertGenomesFromVRanges.R
3567665d2b0fd5f174e691a7e417e9c3 *R/decompTumor2Sig-package.R
a7f3d679ccd8b720d6902ea4d6e099b5 *R/decomposeTumorGenomes.R
f6f4bea03c63849a81f04791b79e784d *R/determineSignatureDistances.R
47c405ff6531567e4c9439d0f788fb40 *R/determineTypeNumBasesAndTrDir.R
b448fa7dcf454bf86a3bc9addda17887 *R/downgradeShiraishiSignatures.R
7f5b741374a561e7ec01c6cd8bafc05a *R/evaluateDecompositionQuality.R
ea6798769853eb8dfad9add686aebcd6 *R/external_classes_wrapper_functions.R
f1d4fdb22974c8791e7afd08b60d9228 *R/getBestDecomp4Ksignatures.R
bd55f33b94c8b2b38f6f7b7b2e2ac687 *R/getGenomesFromMutFeatData.R
da9a0bd65efafb10439a8bc673b31ddb *R/getSignaturesFromEstParam.R
d810f19675eef8974c7f86f9293a8583 *R/helper_functions_for_class_checks.R
fd55048925dc8e6cd68e5bb4774046f3 *R/helper_functions_for_sequences.R
71fdc8909c3491fee35ab0db9b2c509b *R/mapSignatureSets.R
886a863010cc10580873de936ef8eb14 *R/mathematical_functions.R
1f30ae4ed82132620655c204ce17dd7f *R/onAttach.R
91eb48641cda0aa7173cef28b2a5de55 *R/plotAlexandrovModel.R
9196b78ed08284f94becb4275e12eae3 *R/plotDecomposedContribution.R
26deb33f10e188e7924e292d71ba1204 *R/plotExplainedVariance.R
bb4a97a624aba66f2933db262df03f1c *R/plotMutationDistribution.R
a906ef1004658f1e79bcf319bbaa60aa *R/plotShiraishiModel.R
2809646c205bc2e7f1855748c281d5b1 *R/processMultipleSigSets.R
c05b0ddf6535247a6a0cfd1454e4f41c *R/readAlexandrovSignatures.R
55bf20c086a7ad240abf3207d8c8dfa1 *R/readGenomesFromMPF.R
e038bbe8cbbf26561b7b39f148d95088 *R/readGenomesFromVCF.R
7842422438c61564542003e30d03b022 *R/readShiraishiSignatures.R
067047ae1757ea5deb429cac1ca9b6ac *R/setNames4ShiraishiTable.R
8a16254a4caae46bdebb981fc049e97d *README.md
db6d8527169f0744482a5577ceda4bf0 *build/vignette.rds
83be38a8bedee9e97f12557b3cedca9f *decompTumor2Sig-manual.pdf
770d52bdb5b9d73162c507d905ef1fe4 *inst/CITATION
6f245c6383b049770fd7012949712c93 *inst/NEWS
e74785e56f64461db8dd4f77919ead91 *inst/doc/decompTumor2Sig.R
63e12894a233c97e54afeba9cdf4b0bf *inst/doc/decompTumor2Sig.Rmd
4ac76951de57bc0725138c6fb93a1826 *inst/doc/decompTumor2Sig.html
71d5489dca9fd1d3e22149041f3cbcc4 *inst/extdata/Alexandrov_PMID_23945592_435_tumors-pmsignature-15sig.Rdata
dcc8a08c0e2facbdc7d26ed3d2e2f8cf *inst/extdata/Nik-Zainal_PMID_22608084-MPF.txt.gz
99882e3468120514bf5bcfa99e09a8ad *inst/extdata/Nik-Zainal_PMID_22608084-VCF-convertedfromMPF.vcf.gz
c9dc27bb88c4c9d4ff00036ddb81612f *inst/extdata/Nik-Zainal_PMID_22608084-genomes-Alexandrov_3bases.Rdata
ba1243de9778074a4bdc87df3ff9cb72 *inst/extdata/Nik-Zainal_PMID_22608084-genomes-Shiraishi_5bases_trDir.Rdata
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
2500c96364e66fae249f44a3a4eb706d *man/adjustSignaturesForRegionSet.Rd
62e9e638472377c6f12d1b3e062ffcb9 *man/buildGenomesFromMutationData.Rd
eb57207b00cde12b2b180bd1d324d6e9 *man/buildSortedAlexandrovSignaturePatternList.Rd
8d0d036bb2efc368233f5e79ab47cd4b *man/compNucFreq.Rd
dcced11f3a41fa14f65a0e66bd38960e *man/composeGenomesFromExposures.Rd
aab7f33eefcd3068e1b61a790a453273 *man/computeExplainedVariance.Rd
b11198ae86b0998ab82013b159fade12 *man/computeFrobeniusNorm.Rd
b8917bd9e09abe54fb6576e3ee63f715 *man/computeRSS.Rd
8f79b0a1160a531ec42171f9a426870e *man/convAlx2Shi.Rd
0ab68ec62080f7d76dc1a2f92894f360 *man/convertAlexandrov2Shiraishi.Rd
89e18eefd3fbafc751e3c5c8d049afde *man/convertGenomesFromVRanges.Rd
c6d0582500a94d54aeb8091eff2839fd *man/convertSeqFreqToBaseFreq.Rd
07bf38d5b689c5dbd6b27d9cdf98e137 *man/decompTumor2Sig-package.Rd
20cc239814271b6bcf520838fc31f0c4 *man/decomposeTumorGenomes.Rd
9ad7a86145fbb7117b56fd06ef8ba5e4 *man/determineSignatureDistances.Rd
170f0133011724068425b8d84ce62d93 *man/determineTypeNumBasesAndTrDir.Rd
79a834731ffefeb2933493a9a3038029 *man/downgradeShiraishiSignatures.Rd
f504d3d7adaaebdb3c5bebb7c6323f4f *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
4693b5af5a2170ab75cbbbb59b47689a *man/isAlexandrovSet.Rd
e2e276593f5b8d1ce289138364a38d7a *man/isBackGround.Rd
8434ac956cfa74dcd303e15ff21cae6c *man/isEstParamObject.Rd
167bbed04b57a5ab265b5cc904095353 *man/isExposureSet.Rd
75a095cf1ba9b5e6d05491c97819b796 *man/isMutFeatDataObject.Rd
ed6e8a2a516f82e9c7d81cf94d600af2 *man/isShiraishiSet.Rd
40b502b455c88849da497d2789140b54 *man/isSignatureSet.Rd
438cc3e20b96e8ff5a9e3e822f945088 *man/mapSignatureSets.Rd
19ad433381f11716595dc4bf9638875b *man/plotAlexandrovModel.Rd
6814862557d09084d3fe243e8b0449e2 *man/plotDecomposedContribution.Rd
ab4a9bd6f1adff8172d3a1382525e439 *man/plotExplainedVariance.Rd
7b4fbadb724cc21b22cf1309570bd8bf *man/plotMutationDistribution.Rd
7f5e43708c1f64aa457271a904a485c3 *man/plotShiraishiModel.Rd
16f3057bbc25572bb1268a3247505bc0 *man/processMultipleSigSets.Rd
36bc5ac605d55ef4e81f3edcc4c56028 *man/readAlexandrovSignatures.Rd
256e0f84de699c50f8bc68813cb2661f *man/readGenomesFromMPF.Rd
cee1ebdeaced4fbc37064ea6b1b9a162 *man/readGenomesFromVCF.Rd
ebe0ba24198db6cae5da9ab35f0b753e *man/readShiraishiSignatures.Rd
5a7750e977c6344efa84f1e1a371d05d *man/roundIntegerSum.Rd
51df6220f002e85be4b71bb1ac72874e *man/sameSignatureFormat.Rd
1f3cb2006620b6a18d28a64575b728d0 *man/setNames4ShiraishiTable.Rd
36812bd7c01acf4880c6a7a753fce24e *man/setNumFlankingBases.Rd
5758d95ab5f40658211528e15226e954 *man/setSigFeatDist.Rd
5f6e2141a4b4a87632f2751f9a708bf2 *man/setSigType.Rd
e4bc6f3362e7b67aeab38e79f429a81e *man/setTrDir.Rd
63e12894a233c97e54afeba9cdf4b0bf *vignettes/decompTumor2Sig.Rmd
80b89b0a22426bb979abeb75b50afa4e *vignettes/example-sign-Shiraishi.png
