badc7273aac1fe7444290946bf7d2548 *DESCRIPTION
c8288521cd308fc2dbea999ac2b1929a *LICENCE
cd97df4080cedb8434313ed2c57430e4 *NAMESPACE
c7d9e7b4a6908a90eff98b922785792a *NEWS.md
906a20b9427a8018433eb4ef3ba475d6 *R/asserts.R
f404f4fdec9123bbef2a24917123cf09 *R/class.R
debc0094ef7b772f418b1707ff3d87b9 *R/data.R
87e57e56e006e03accc68de089ed991b *R/global.R
ca35c56c0c379f292f8fab68b3a19f61 *R/midasHLA.R
43236b9c8bcf96b132b070e98ac5385f *R/parsingFunctions.R
bcb487cdfc7cdd7929b7e7fe2b746521 *R/stats.R
cd46d4ba657597f79bab29fc0ba19acb *R/summarise.R
76243d7f28d13753ffc6add954d2e5ef *R/transformationFunctions.R
489fdb912ee86a636dd88608de903a71 *R/utils.R
9166d66d5b9ecf84ef41a8852367ae32 *README.md
dadb3d0342413e1a1630d631b647fa1c *build/vignette.rds
22c36a976b688063e8e03bf5710262d0 *data-raw/MiDAS_tut_HLA.R
a6c254b8f09cf8346d2071fe86f250f9 *data-raw/MiDAS_tut_KIR.R
ca5dc825b1b7f9035cd047957aed8133 *data-raw/MiDAS_tut_object.R
5c0e02b1f82d81a6a50909f478321721 *data-raw/MiDAS_tut_pheno.R
c110838b23bc42ee40100d91b248b902 *data-raw/allele_frequencies.R
f70641e0b533903d67c2fc897e5c789d *data-raw/dict_dist_grantham.R
4f13afe858ac68ae406fb786fc281ca0 *data-raw/kir_frequencies.R
18d068ff1486895ada1217730947c5b2 *data/MiDAS_tut_HLA.rda
2ef2230ee87dadf7ab1f6c2d2932919f *data/MiDAS_tut_KIR.rda
537a46a2efda98d912d0ecb54a77ea05 *data/MiDAS_tut_object.rda
81909efe566303a3ff8657d12c616a30 *data/MiDAS_tut_pheno.rda
652174b12bcd368d6ca74b1c78d705de *data/allele_frequencies.rda
9c476e8b564bac93dc3fb9b913aedadc *data/dict_dist_grantham.rda
b41b6b51cabe30c4353bfcad0751b98c *data/kir_frequencies.rda
eea56b7f1c4737f1b159334fa15c80d4 *inst/benchmark/prepareMiDAS_hla_aa.R
4175500f3b151ecc16b1a5abef7c3e69 *inst/benchmark/prepareMiDAS_hla_alleles.R
de7e4687b3d27905577392616dbeca78 *inst/benchmark/simulateHlaCalls.R
c2ef4f521f68878cb8c6cb15d3eb1c40 *inst/benchmark/workflow_hla_aa.R
f4c769612ed04a0639977212ffd089c8 *inst/benchmark/workflow_hla_alleles.R
7871f7481f8076772f136429ad225d12 *inst/doc/MiDAS_tutorial.R
3928d2cd35e119e79963aa95d6f1257a *inst/doc/MiDAS_tutorial.Rmd
6e6805200ed2ab07638c193dda631965 *inst/doc/MiDAS_tutorial.html
087b348df6c5da4b3fee7b2accec8958 *inst/doc/MiDAS_vignette.R
344a60f787274b5f4aa79724ea89fa41 *inst/doc/MiDAS_vignette.Rmd
7ba61d0b8802e61becad480565407b7c *inst/doc/MiDAS_vignette.html
8ed469ccb70fb2c717deefc1fcad6a51 *inst/extdata/A_prot.Rdata
0f68d661405a0b2864acb00d3066de0e *inst/extdata/B_prot.Rdata
a5a97154e62c0a89538877d297f69b48 *inst/extdata/C_prot.Rdata
50f68655c0c61b83c77ec3681f9e7a4a *inst/extdata/DMA_prot.Rdata
26b2fec706e4f31680d1bfb2dddf261c *inst/extdata/DMB_prot.Rdata
2e3894086fa9b2ab3c39eec025e3013c *inst/extdata/DOA_prot.Rdata
00e84beae1bc93e476f8986ea2f2307c *inst/extdata/DOB_prot.Rdata
a2040f3d011cd04aee3120b26567f208 *inst/extdata/DPA1_prot.Rdata
8dac6051579fcb8a4a133aa467b4adcd *inst/extdata/DPB1_prot.Rdata
078f4b01257c471cc72b3838600b9e28 *inst/extdata/DQA1_prot.Rdata
e95c2be193cbec06d8da7f373d0a3ded *inst/extdata/DQB1_prot.Rdata
db452d83a64da051cecd515e33faac06 *inst/extdata/DRA_prot.Rdata
41b0cf04877d8924861b271298470630 *inst/extdata/DRB1_prot.Rdata
ce83251037b320e1b22ca63e8e72274e *inst/extdata/DRB3_prot.Rdata
114d0bcaf12590063e839b43ccffc0b6 *inst/extdata/DRB4_prot.Rdata
84827bc86ca51e9d887f555d3695e7fd *inst/extdata/DRB5_prot.Rdata
07ffaa637bacf64ae0f4b8be93acb2b0 *inst/extdata/E_prot.Rdata
ff1a40cea5738b277f6a2c056933fa8d *inst/extdata/F_prot.Rdata
9bc820939ab075d331e6ec541e12819a *inst/extdata/G_prot.Rdata
5deae2ba75f0bed4e7908a9db7890a79 *inst/extdata/HFE_prot.Rdata
85fbf3b8dc0a51cfe717b49da2d0bd1f *inst/extdata/MICA_prot.Rdata
403f6f2d41b66f33a3906457ce9a0d6a *inst/extdata/MICB_prot.Rdata
f2e31e1899d80e8b4fb8d86443baee8b *inst/extdata/Match_allele_HLA-Bw_only_B.txt
8766a626e638a8415d4795d431420d36 *inst/extdata/Match_allele_HLA-C_C1-2.txt
2a611bbefa22822411159738fe7a723a *inst/extdata/Match_allele_HLA_Bw.txt
1441dcfccdb437271124fc1cd56393b7 *inst/extdata/Match_allele_HLA_Ggroup.txt
44c00b2b003a7b270a161871b85027a1 *inst/extdata/Match_allele_HLA_supertype.txt
7f33e0a29f5394acba46174257b28a23 *inst/extdata/Match_counts_hla_kir_interactions.txt
dead200a7cde07cf8860f1c5267c5ff9 *inst/extdata/Match_counts_kir_haplotypes.txt
4e6966a68e4c8bd7434bc2a56cd5e716 *inst/extdata/Match_kir_haplotype_gene.txt
2d741ccc9ebe79dcad4aecbae3436327 *inst/extdata/Match_kir_nomenclature_gene.txt
20695da4b6ffdadf6f603f8d45a07ca2 *inst/extdata/MiDAS_tut_HLA.txt
3f0474e53e2acb36ea2e357d192bb644 *inst/extdata/MiDAS_tut_KIR.txt
259d542308722e5e5552c4e6b5fe5787 *inst/extdata/MiDAS_tut_pheno.txt
fd1034516e21e132795ca22563229da7 *inst/extdata/TAP1_prot.Rdata
2de8ac5aaa37fcd09b2a5bad1b7a0bcc *inst/extdata/TAP1_prot.fasta
099daba8d0fcece1df009ca4918ec04a *inst/extdata/TAP1_prot.txt
30621541cdec17e6a98ac94aa54f98bf *inst/extdata/TAP2_prot.Rdata
b2bca0a2d1709a468b5bd194e9639663 *inst/extdata/grantham_distance_matrix.tsv
146aabcd4c3187b3964be86b09d039aa *inst/extdata/test_Match_4digit_supertype.txt
a46797042a43c9d90d3535547b8e52ac *inst/extdata/test_aa_variation.Rdata
2d316c6a61c266d88bf154e943cea82f *inst/extdata/test_hla_analyze.Rdata
305f183b151d64a9af4e538ea46584e4 *inst/extdata/test_hla_calls.Rdata
932c24c1eb50ecefddee6c0e66b57878 *inst/extdata/test_hla_calls_res.Rdata
1f66674fd923cead4cf3cc8fdee6d145 *inst/extdata/test_hla_kir_interactions.Rdata
fdd5aeb90d7e9db319fcc6113ed6e211 *inst/scripts/download_extdata.R
f429d584b4143f1a92d44d1159c31c0e *inst/scripts/parse_alignments.R
6cc2c1ecebac286b2289ff109c4372cd *longtests/testthat.R
ca16b26f29387cbc1a18d53f404c4c87 *longtests/testthat/test_class.R
de38d7c731c2b915775b5394a7ad6f9f *longtests/testthat/test_stats.R
427750084f5a377317bfeb3a3eadba37 *man/HWETest.Rd
3e371674aa5273f14c1bae3782bcec31 *man/LRTest.Rd
425b7244cf0dc3ca65f7bc6c4afeb055 *man/MiDAS-class.Rd
b361719f3498f179457625244d0e231f *man/MiDAS_tut_HLA.Rd
a2ec1f091e2a2638800999a8acb2de78 *man/MiDAS_tut_KIR.Rd
08f924484fadbd0de899bfd5916004c6 *man/MiDAS_tut_object.Rd
1b945faa92c504b5a3892542663adf35 *man/MiDAS_tut_pheno.Rd
ad1f1d706d8a8312026f5ca4158cd59e *man/aaVariationToCounts.Rd
2dbdcf0c898011e9e8eb88c46b175318 *man/adjustPValues.Rd
e17700f9dc974602a4f749dc8e46d650 *man/allele_frequencies.Rd
eea551b1d3e7331a573dc3339e0d7f05 *man/analyzeAssociations.Rd
05cf7713d1246ea0e9d481f676f79244 *man/analyzeConditionalAssociations.Rd
70c800f331b76fb8536dc24b83a00f73 *man/applyInheritanceModel.Rd
ced5ead43d8ab101a783a70f9cebd2f5 *man/as.data.frame.MiDAS.Rd
92609ce511ba31461f60506648903380 *man/backquote.Rd
25ec4996bbfc8333b218ff9c97adfb7d *man/characterMatches.Rd
ea5e5023e680d458ad911ad7c3001361 *man/checkAlleleFormat.Rd
b6496fee072bc487d755c1a1c3a87859 *man/checkColDataFormat.Rd
01357003c7ba47757a43de8fd2494db7 *man/checkHlaCallsFormat.Rd
238a32c28bd5a642f13ca63db556e4eb *man/checkKirCallsFormat.Rd
07f520c315af3a21c0014a4a9c368b1f *man/checkKirGenesFormat.Rd
3aa65e9abc1be2e9d53edc8df2831f51 *man/checkStatisticalModel.Rd
b885d60442dabc492bdae4a58e61a27c *man/colnamesMatches.Rd
d00a4632b68d57b4ec1dac805b1c6ed9 *man/convertAlleleToVariable.Rd
e2ac109929c465287fc7408db7babfaa *man/countsToVariables.Rd
7673c61db9bc0945080021bbc5872436 *man/dfToExperimentMat.Rd
abec8d7f8a370648327be8410a82718b *man/dict_dist_grantham.Rd
21428f2b706a70166da856025697d811 *man/distGrantham.Rd
83cd2055b3a8904c9831f0918baa46ac *man/experimentMatToDf.Rd
f238733e3aa04e4edcffce2148a476bc *man/filterByFrequency.Rd
d541567dd78e7a29f111d48fe6c5d889 *man/filterByOmnibusGroups.Rd
02a3077106aad2bcd8d19357282605bf *man/filterByVariables.Rd
c8117fb60759e30f40aa8429350d1aaa *man/filterExperimentByFrequency.Rd
249c56ec9c101d4c7a0ef71097040a16 *man/filterExperimentByVariables.Rd
2d4d270d90ce072454e592706996707f *man/filterListByElements.Rd
75973ee3e2b4accf9cce9c7b74c22aa8 *man/formatResults.Rd
ec536aac492ee3515b8c8c9caf31159d *man/getAAFrequencies.Rd
69e24f2553261b8b199c2a622b111fe2 *man/getAlleleResolution.Rd
46c59cbba256549e5acb585af238d52b *man/getAllelesForAA.Rd
e07075c1e8186e0f26f7081ccb8b4c62 *man/getExperimentFrequencies.Rd
c1c36cfb11e0a931f10bb4fd5c7a6780 *man/getExperimentPopulationMultiplicator.Rd
888aa22475ee874c38314dfb0548d27e *man/getExperiments.Rd
473cd6967b39eb60ec6972a17d6d200f *man/getFrequencies.Rd
6f4104d4e2829dbd2add76343f7afe37 *man/getFrequencyMask.Rd
80566bc10bfba28b70873a44a3dafc9d *man/getHlaCalls.Rd
fc13e6aace1f90801bdab71d48bb0d22 *man/getHlaCallsGenes.Rd
267fc9f4287a26cf5a40b62725fc6c49 *man/getHlaFrequencies.Rd
1e59fa8d37bfae8c34e3ed8b416f980f *man/getHlaKirInteractions.Rd
b19f86e50506d444f6e3fa5c80c0d2c1 *man/getKIRFrequencies.Rd
d4ad0bd4c5f37c3b9cc0a07d1aab2cff *man/getKirCalls.Rd
5849218b5f7f12bce55422ccd574c315 *man/getObjectDetails.Rd
30f90e01878dedd633f35c228e257fd6 *man/getOmnibusGroups.Rd
0130aaedf57baf1553b4d190f2d01ba0 *man/getPlaceholder.Rd
cdb52e7b0f0ddc351580affc9a41467d *man/getReferenceFrequencies.Rd
0e788e86c8f32f2ccd5b048d49e87fdc *man/getVariableAAPos.Rd
6a2c1c465543b626ec14b89132d48744 *man/hasTidyMethod.Rd
089ce1886c93c35dd3c0de5e310a112a *man/hlaAlignmentGrantham.Rd
a840eed503ec80daee5018556ff9540c *man/hlaCallsGranthamDistance.Rd
4c9fe6129551089809d7a4dc9e92a477 *man/hlaCallsToCounts.Rd
e9dac6cd29d00477513a7ead12e804a1 *man/hlaToAAVariation.Rd
cdd3b9a1f666546803fcb2dee5d2e96f *man/hlaToVariable.Rd
c255d7b2c81fef7fca72c3b2f0ad9e10 *man/isCharacterOrNULL.Rd
6dbcf743cc6c020fe62ab775f732744b *man/isClass.Rd
cee58245e920f1ea722eb6b81c9db0b5 *man/isClassOrNULL.Rd
e7a05ab24dcceca3d25bf58a0b8a7ec8 *man/isCountOrNULL.Rd
5f4e97f33e569fcd327ecdd25378a277 *man/isCountsOrZeros.Rd
737ce50ec690eb6ebca39705a2ffacd4 *man/isExperimentCountsOrZeros.Rd
bceb4db76ee87ab613684ff42abeb373 *man/isExperimentInheritanceModelApplicable.Rd
4423f85db5447c13ff3367a813b3cddb *man/isFlagOrNULL.Rd
e1e59279b5933557603176859fd3b645 *man/isNumberOrNULL.Rd
6f7f2af981d3831c667cf0ca70c8074b *man/isStringOrNULL.Rd
06e9f42b81c02a540a8e9dc274606135 *man/isTRUEorFALSE.Rd
f4f0f6ae330521ae5fcb37e024411751 *man/iterativeLRT.Rd
c3be25d8506696cfd55edf1973893599 *man/iterativeModel.Rd
f428d3c7937ede283e332db046b6bb82 *man/kableResults.Rd
ce759865d80e012294e817228ffd2e07 *man/kir_frequencies.Rd
c58858253e6f47dd7b94b50b3d1a39a7 *man/lapply_tryCatch.Rd
cf90f7b404774d0024a622f774ac1a97 *man/listMiDASDictionaries.Rd
582f40b8c73af9d429005849ed483483 *man/midasToWide.Rd
3f1c5fcfe707a95c93c61ac630a63bf7 *man/objectHasPlaceholder.Rd
c6b560ae1e70675fcc4f8202ae1aad0f *man/omnibusTest.Rd
e6a3bfcc5dd76cf5e40e09b0b2f855d5 *man/prepareMiDAS.Rd
45eff6e1a89371a480310fea6259d266 *man/prepareMiDAS_hla_NK_ligands.Rd
f4ae62da8b5bf8e7a5b6a223a79e1093 *man/prepareMiDAS_hla_aa.Rd
9147742da2eae683128445889d7ced5c *man/prepareMiDAS_hla_alleles.Rd
472ad27b6ad375ea1d032606f027356e *man/prepareMiDAS_hla_custom.Rd
6d7f5b5031161592ce84dfccb8178953 *man/prepareMiDAS_hla_divergence.Rd
8df335f983d9479e50abb99678db9a07 *man/prepareMiDAS_hla_g_groups.Rd
bc74ba423b5deb55314548bed26b538f *man/prepareMiDAS_hla_het.Rd
bc788b0b4422884be86104f49f3fdab6 *man/prepareMiDAS_hla_kir_interactions.Rd
09b7f8c69f6fb9900ebb1ab88fe0ee28 *man/prepareMiDAS_hla_supertypes.Rd
137e5daf6217c54593ab7f5acbacddf9 *man/prepareMiDAS_kir_custom.Rd
be3e390b87bf37b4163d7fefd1a7cd4f *man/prepareMiDAS_kir_genes.Rd
8758d0cdad347d3a635ae4ade4c4efa1 *man/prepareMiDAS_kir_haplotypes.Rd
920b61da8f482a9f7576ea163bd52f20 *man/readHlaAlignments.Rd
e0801614abd91bf5adb7daccdf717327 *man/readHlaCalls.Rd
872a36dd1ca1961d7c49fda5110d2f3f *man/readKirCalls.Rd
4bfae845a7b63b0c4a1001da40e2e35e *man/reduceAlleleResolution.Rd
39413b25540037ae6b78dbca32a0c13d *man/reduceHlaCalls.Rd
d2246b8f91655ab95cf90b743acdd779 *man/runMiDAS.Rd
c2df09810c7ee6a0ea14c0e5b8f5d1b8 *man/runMiDASGetVarsFreq.Rd
2124193f94d7f6acdbdd68ac405a656d *man/stringMatches.Rd
71e7c1d81b7467f73c641b5f442ac428 *man/summariseAAPosition.Rd
6e36b537292262e55b11c6b88d21d0c8 *man/updateModel.Rd
9726a77cc8729fc90e4e13f86f102d26 *man/validateFrequencyCutoffs.Rd
ad7c59d7ecf3c1bef31ab17a80ebdd90 *tests/testthat.R
f1d797c40688c3e655c6d3d587812669 *tests/testthat/test_asserts.R
adf7a8e96ed2ad293852159321b3c15b *tests/testthat/test_class.R
1efc8bfe0d0017f6ae24038e2920c5af *tests/testthat/test_parsing.R
15c1ab1119661770eb97aeaca0d2f37a *tests/testthat/test_stats.R
a406b3e19683630846f47de8c45bb6ff *tests/testthat/test_summarise.R
cf6c13759eeae3c95046283056ae746b *tests/testthat/test_transformation.R
94407874df47776f91aae867ff225055 *tests/testthat/test_utils.R
d27b9c4c790bf5b581a810b0638ef30c *vignettes/MiDAS_logo.png
3928d2cd35e119e79963aa95d6f1257a *vignettes/MiDAS_tutorial.Rmd
344a60f787274b5f4aa79724ea89fa41 *vignettes/MiDAS_vignette.Rmd
