16b96e0334eec520624992bbe62e5724 *DESCRIPTION
37eb962061c5ceba7a85f0a1f04fde17 *NAMESPACE
b3a7f08a4cf98e151d07b3b3574a0641 *R/AllClasses.R
660497bedb7a605ab29a5a6aedc58346 *R/AllGenerics.R
eba9002a30f0e0bc41d55f4cdb3c005d *R/BAFfromClusterMeans.R
c776be3b10a13df1f51a6da7bf0f683f *R/BAFfromGenotypes.R
09fb3379791dae67ba65ca691e34624f *R/LOHfind.R
e50d353abe0ddd5171d60070a8a09d59 *R/LOHselectAnoms.R
f3a3981e3ba3533b433cc826250bfb0e *R/Methods-GdsGenotypeReader.R
a1485a77eaf0933a2cec979f762694b3 *R/Methods-GdsIntensityReader.R
e10db0092ef81989a9271d944e4cbae6 *R/Methods-GdsReader.R
c187825fc3d3bfe984165e380f992e1f *R/Methods-GenotypeData.R
2416d0de8aae4e236f74493126c2141e *R/Methods-IntensityData.R
f9f96f2b6c27afd6396b779f0f85cd09 *R/Methods-Iterator.R
ba2c7f1d9a75f5c3f6277e48d2ec0443 *R/Methods-MatrixGenotypeReader.R
d97b28a9f36d2fc5bce6775df1fc0e53 *R/Methods-NcdfGenotypeReader.R
0d459900acdb9463584d9b9213f315a1 *R/Methods-NcdfIntensityReader.R
29188e44ad2b79630d8bc9f7e38909f1 *R/Methods-NcdfReader.R
76310c7dff93c890fe362561cc139d63 *R/Methods-ScanAnnotationDataFrame.R
a95d7281529a47577ed8620f186b4c48 *R/Methods-ScanAnnotationSQLite.R
a76a8a05521a0d151b163d28761d5cb4 *R/Methods-SnpAnnotationDataFrame.R
9b3d757f05ac19068e5bbaf38864d114 *R/Methods-SnpAnnotationSQLite.R
b1c6c5c33100044a1109ded2364ba4a2 *R/alleleFrequency.R
dee0b753b9207d53d75316747b6f87e7 *R/anomDetectBAF.R
0d8451662f4a23b1a70fdaea988a7a15 *R/anomDetectLOH.R
ed59fcc8b8cf0fbd208045b2024371c0 *R/anomFilterBAF.R
293d1a75c669dc197c382e5ce24f3db7 *R/anomIdentifyLowQuality.R
8768a4866bf3fdb8886b02c5c9279744 *R/anomSegStats.R
013ff565130c5a15c841ee9d0af4b8d7 *R/anomSegmentBAF.R
86ec56d04146f176cae9be896ec045d7 *R/anomStatsPlot.R
d887de9806d76f0057882d0b0a959d90 *R/apartSnpSelection.R
c9efa142ff8fc9abc2a8d731095c1fd9 *R/asVCF.R
2ea7825ec1a5c717236b4a84f7b5e612 *R/assocCoxPH.R
a36fc6e88d1b71e729d9d5f4a96af8fa *R/assocRegression.R
2bcbae3bd063f14a0152ea3918f6ee20 *R/batchChisqTest.R
a83074d5ce06dbdff0e219653d412db2 *R/batchFisherTest.R
02bcfb748c7d6601d44cc35808dfc85b *R/checkGenotypeFile.R
650e7bc21a18100a761bc41a3987d405 *R/checkImputedDosageFile.R
86a5be7938b292809c3a42f4e80c3c7d *R/checkIntensityFile.R
5875e82f5ddb9e04172cc2b25205a9c7 *R/chromIntensityPlot.R
7fb32c0aa393cfea48aab1e66f89e630 *R/convertNcdfGds.R
437249b9344f2c2ca6afe03c20d03035 *R/createAffyIntensityFile.R
f8b01e35363111a492f94a2670419e50 *R/createDataFile.R
f7fd76960bf42222464782d31c6c55ab *R/createDataUtils.R
c452ad311042018812742a11c4f0787e *R/dupDosageCorAcrossDatasets.R
7ac3e99437d5ccfa234767b7c29d93ad *R/duplicateDiscordance.R
a8bdb3d8ffcc41b28ffa92244bf90767 *R/duplicateDiscordanceAcrossDatasets.R
f49bb8852470c329d28b50494273b052 *R/duplicateDiscordanceProbability.R
738490ab684144821d872b45aa9b3321 *R/exactHWE.R
78763442ff4a022465feb1af7b6cd484 *R/findBAFvariance.R
8c65b8237f88f56f53924bc40fac46c0 *R/findRelationsMeanVar.R
df147c7adc7050533b25a424d56eca11 *R/gdsSubset.R
362e2432c449487e922d4242cac87ad4 *R/gdsSubsetCheck.R
5688198fc97284a62da7d55a83b49cc4 *R/genoClusterPlot.R
5429fcc1ac20c19dd3adf27329f2365b *R/genoClusterPlotByBatch.R
883fde8bf09815829fce17023d23c455 *R/genotypeToCharacter.R
c69dac892f72e2433fc3a8d9c3c0d84b *R/hetByScanChrom.R
ae5b5a9ee064f8dc4105eb57aabfc943 *R/hetBySnpSex.R
068b81faa015dec6efdf525777f12f48 *R/ibdAreasDraw.R
c258fa793c5d812fe80b46b8ccba71b7 *R/ibdAssignRelatedness.R
7d826075f7ebb7f8ab7b2f08c4ac03df *R/ibdPlot.R
b60d682c3ef3761760da48630c8791ec *R/imputedDosageFile.R
6c47b804a362201231584f2fe2ac649d *R/intensityOutliersPlot.R
a5732981fef72644c2248290159ee89a *R/manhattanPlot.R
bd7e5d13ded83eb8f4fd347d35102869 *R/meanIntensityByScanChrom.R
ffbb3c29828bd7e7cf1ba469f80b4317 *R/meanSdByChromWindow.R
3c50ca4f88d3e2fa187ee75e4da3f965 *R/medianSdOverAutosomes.R
0b6d0d789e58e1bbe975ee1857efd2f9 *R/mendelErr.R
8517236c632c06725f0798a1217e36cc *R/missingGenotypeByScanChrom.R
1f305607402775708dc2a8192b92f366 *R/missingGenotypeBySnpSex.R
2415cc9a77b562220de726c9df70c910 *R/pedigreeCheck.R
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da7897b87eb2ee1ba9670595d7494d20 *R/pedigreeMaxUnrelated.R
10586e2d27c58fb2a3ecc35ac9187fc3 *R/pedigreePairwiseRelatedness.R
03dcaf96bf5f0236cf1ebed5f4ae2a76 *R/plinkUtils.R
0304df269aeb5412764c7bc120d43d9a *R/pseudoautoIntensityPlot.R
9cbe3e4a9f9f2f9d30b6bc6cc3cf153f *R/qqPlot.R
abeeaf532638fc488b75f61e9ca84ae5 *R/qualityScoreByScan.R
7dc13c7b95e8b1b86aa91af8d983cfd8 *R/qualityScoreBySnp.R
eb3025a2d1d2f1305a6c17c8e9d2b26e *R/sdByScanChromWindow.R
e918ddc819be55d6d9f0f5ae1d2a24d3 *R/setMissingGenotypes.R
5d54b07df3d7c7f11813d8e680345b9d *R/simulateGenotypeMatrix.R
2628de7541c197f178c59ee391b8e3af *R/simulateIntensityMatrix.R
5325e83d0c2a4a926af9c1d352029254 *R/snpCorrelationPlot.R
3311b141aa38de14d97c1f103284463c *R/snpStats.R
8c3f33df4e1032bcd81b7fc1a89d7905 *R/utils.R
4ce60b81436cee423b6b2aae93414fe6 *R/vcfWrite.R
b7f8b6026e73cb737b1afef4f1da7ec8 *README.md
59b5518d7b70de27f886680282fb4042 *build/vignette.rds
4a17bd862eefb22195861076a5992211 *data/HLA.hg18.RData
9281ae3bcdb734fe2eef3864fdf86537 *data/HLA.hg19.RData
7b7f233d9a6f9f7c0030d579cced8851 *data/HLA.hg38.RData
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8c32910bfafa2a4aa98f67f00d97bb27 *data/centromeres.hg19.RData
5d3e0872245641e857615645381d7ee4 *data/centromeres.hg38.RData
9fd45148cc848551e5440f6391ab576a *data/pcaSnpFilters.hg18.RData
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7d28e2d309e5d3f63e4c96e7f075cad2 *data/pseudoautosomal.hg18.RData
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121662f7f8862fcaa14e6e029ee3b63b *data/pseudoautosomal.hg38.RData
18961c4ae51dd493fb7a17b490f430fa *data/relationsMeanVar.RData
86ac0f4f0f0d6a8ae11dfa33bf9c93bc *inst/CITATION
767fb55d426754d9f6bcd935e53b3933 *inst/NEWS.Rd
cd1c571e93c7ba4710a759ee333437b0 *inst/doc/Affymetrix.R
ea0cc40c4fc8dad38a19a7136ae65273 *inst/doc/Affymetrix.Rmd
4379180c7461ca399697b9b96a31375b *inst/doc/Affymetrix.html
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0e461ad50462bfc084a03d0b531e8ced *inst/doc/DataCleaning.Rnw
05ae6bd7c694a6be05110409940a0fba *inst/doc/DataCleaning.pdf
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3ed8a3c2cace9a052c7b15334eedbe81 *inst/doc/Formats.Rnw
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97f3f44a2aec8d48f599eba2ccb40664 *inst/unitTests/BAFfromGenotypes_test.R
64973c474d2255c248c0b073b56d55bd *inst/unitTests/GdsGenotypeReader_test.R
a63cc62a797d9091d8a8fe079b234922 *inst/unitTests/GdsIntensityReader_test.R
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57398362ee4a3abeff7db5717d36828d *inst/unitTests/anomDetectBAF_test.R
dc188b62be9fa7f6cb0cb54f5ecff29b *inst/unitTests/apartSnpSelection_test.R
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4875e8e180fa4c7508a8af7ca1c7f21f *inst/unitTests/convertNcdfGds_test.R
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905598138226fdc90c7e5bd3f553c024 *inst/unitTests/findBAFvariance_test.R
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31845f58eebc2ed69ebc66984629766b *inst/unitTests/missingGenotypeByScanChrom_test.R
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7e5552ded02655b72a473d52713859ed *inst/unitTests/pedigreePairwiseRelatedness_test.R
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3b8010c632f8310f788e5eb00ad4ae31 *inst/unitTests/snpStats_test.R
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63e6fbdfebcd0705b42a20eda7ab3574 *man/BAFfromGenotypes.Rd
336665a8ef9e13af36122543a410c4bf *man/GWASTools-package.Rd
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2ef8748155cd70c3f5d52e48d017fdb6 *man/GenotypeData-class.Rd
920a0afac609d7541834db37d1a26e64 *man/GenotypeIterator-class.Rd
661d7f2a16b5190c5e9de0727e2e4cf4 *man/HLA.Rd
04968eb0a5601a277e9d556e2133a172 *man/IntensityData-class.Rd
9237e340018aa54bb6261f40979a7413 *man/MatrixGenotypeReader-class.Rd
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8f6d8cd0537b86f1e8856c7d8d4de347 *man/NcdfReader-class.Rd
36ce7306119ce8fee53e9c5431d5e618 *man/ScanAnnotationDataFrame-class.Rd
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5c993cebb0f899bb18d8055a3c7e117f *man/SnpAnnotationDataFrame-class.Rd
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91eb3ad904cc3213cfc9fbaf304b9be8 *man/createDataFile.Rd
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65f7bd5ead0527fb6dab0b3ef937d828 *man/duplicateDiscordance.Rd
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56810b4736d9ebb1e40af78c2340b19a *man/duplicateDiscordanceProbability.Rd
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cf9f011b2eb5a8edfc857e0c23bb5292 *man/genotypeToCharacter.Rd
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36fba51f51a7afd48abda687967dfc9c *man/getobj.Rd
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bc9bb2979408ca558151dc522e79d41d *man/meanIntensityByScanChrom.Rd
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9d50207be23e63cdd0813b160beee4f7 *man/mendelList.Rd
9cef19fbd28f2a5c8aec69a55fe607fe *man/missingGenotypeByScanChrom.Rd
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e9eb75c6a484c1d351ec98b547932b6d *man/pcaSnpFilters.Rd
4a6dec11f9d298261968c0b79cb1a5df *man/pedigreeCheck.Rd
2b9f16a641779b802f69faa5ad3be2ff *man/pedigreeDeleteDuplicates.Rd
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6eb9007640642dd25837962447076abb *man/plinkUtils.Rd
6c64ff86aee377f6d3a356a6addd67dd *man/pseudoautoIntensityPlot.Rd
178d07672c2f4f4d19556385de84a159 *man/pseudoautosomal.Rd
3bcf4a6816b2ab55714351604467d1ae *man/qqPlot.Rd
bb264b60783c65d3e81ea43c0d639a67 *man/qualityScoreByScan.Rd
87691b78e5301b67dbba3bc8e145c93f *man/qualityScoreBySnp.Rd
58933cf8fc0a8a9a3a6f42b28a33103d *man/readWriteFirst.Rd
582b2181fd125d6b1acbda9da4a83020 *man/relationsMeanVar.Rd
f833d1d70fa93ef2706a2c7b4ee14850 *man/saveas.Rd
2cd87c3fd165c80cd24f2147a86195e2 *man/setMissingGenotypes.Rd
2e1f4fa51677f2dfaf8dce10295a2dbb *man/simulateGenotypeMatrix.Rd
2e551a3634835b47df1189b3c50162a9 *man/snpCorrelationPlot.Rd
5a20d2a95dccb76cc0a2045357b4216e *man/snpStats.Rd
f8905851ddfcd91cb448e340a71b7cf7 *man/vcfWrite.Rd
357b6e852ce6f97e02f2ceccf7ab94c8 *tests/test.R
ea0cc40c4fc8dad38a19a7136ae65273 *vignettes/Affymetrix.Rmd
0e461ad50462bfc084a03d0b531e8ced *vignettes/DataCleaning.Rnw
3ed8a3c2cace9a052c7b15334eedbe81 *vignettes/Formats.Rnw
