e3a4f30b09a45cd403394beccea32760 *DESCRIPTION
76fe35b487449e3308a9a4f6c406cc42 *NAMESPACE
b7166566ea33a56ed2853796ccf8f415 *NEWS
63d0d445d9bf278b4962b62dc510c5e3 *R/ASEset-class.R
930501a36dd9e0b0a20721e2fa5e9b77 *R/AllelicImbalance-package.R
ae37a8a236580f5ea38730c6b085934b *R/DetectedAI-class.R
ab3870f6d7977bb9026656c6997fbe2e *R/GlobalAnalysis-class.R
130db90796d317960e991a2e0f3c0655 *R/GvizTrack-methods.R
687c6bf01ed4babaee66e966c5a43c26 *R/LinkVariantAlmlof-class.R
c1e030843e0b80b19faabb2e8aa305e4 *R/RegionSummary-class.R
cc60859cb4623a297cc718eabadfed27 *R/RiskVariant-class.R
fa0a3b1e55772daa92bf63e9957c5ab8 *R/auxillary-functions-annotation.R
604ff28160b63b526e35bae81b98497b *R/auxillary-functions-visuals.R
d41d8cd98f00b204e9800998ecf8427e *R/auxillary-methods-annotation.R
14a60be632c0a77fd795248c4ad5e8c8 *R/auxillary-methods-summaries.R
0bf5c438385de32d3dd58e9eb1653e27 *R/auxillary-methods.R
c403c6ce1e6e48844701ed255dadc2e3 *R/barplot-methods.R
a77ddd590731dc441580fa7f31fc29c2 *R/binom.test-methods.R
5d8e7f645aaac01ec6d99a64b0903f2c *R/boxplot-methods.R
081828731f50825a3f232e409c1ad58f *R/chisq.test-methods.R
042675d18f1e617c899fb1591b65018d *R/deprecations.R
05caceb1dd543fef358c62168038f5f8 *R/detect-methods.R
3203df10a5ca317168741e410aabea3d *R/filter-methods.R
2763a8496c923de879372f4ca3b69fae *R/histplot-methods.R
236cc393cf14e9151864bb5b05fc8c20 *R/inference-methods.R
03b8633a04769fae43dc3ef4a11d1d34 *R/initialize-methods.R
bb3e345f83e605ce51dddb49c54057d4 *R/linkage-methods.R
fffcc905da9b462c7b72fe7469680080 *R/list-methods.R
6f5e3d2b1c6627250c8b9a26a013037b *R/locationplot-methods.R
e3a45af72c3609ebfe55b5c8686b27ba *R/mapbias-methods.R
aadbddd4bce1de0f3981694fb2519837 *R/plot-methods.R
0ade052ac1b6ee0c776529549a31b9a1 *R/show-methods.R
3afad8c14c397d8c1586fafb6b1b4746 *R/simulation-methods.R
0b8841fab6ded70f9505a2ef6f902384 *R/summary-methods.R
02cd29ff89b0f5a7b20aded462dd075b *R/utils.R
531755c53f2f8b1f78a26ce4a5f3f1db *README.md
824a9ddcaf0c7fb4baf149caf8617355 *build/vignette.rds
2aa705d823c5c2a8c05f863bf388cc38 *data/ASEset.rdata
3cefc6fd868c57027b7063cb2afaf91d *data/ASEset.sim.rdata
6e755f1bed902ec4d4fff3c9d2e4e231 *data/GRvariants.rdata
0e3e43ed2a6860b0e72e5972cb3307ab *data/genomatrix.rdata
30ca30ad7ad9c59981cd6bdb54add17b *data/reads.rdata
2d5e04de5e4e40b28917147d12a4da8c *inst/CITATION
e095a27e876c6c84df33ce52ca8ca2f9 *inst/doc/AllelicImbalance-vignette.R
5e35b2e9a659f3dab6f8df1d5f3ce221 *inst/doc/AllelicImbalance-vignette.Rmd
9581e73974d527f40d9e1fe596921e4c *inst/doc/AllelicImbalance-vignette.pdf
d0e3895e99e05e2f7be3f8d456ba1d1d *inst/extdata/ERP000101_subset/ERP000101.bcf
71b6e8424a8f798642e733fdde626de5 *inst/extdata/ERP000101_subset/ERP000101.bcf.csi
67652f778d3983f39455d1afe802aa47 *inst/extdata/ERP000101_subset/ERP000101.vcf
b2434dbd4216e78744de4183be5bd879 *inst/extdata/ERP000101_subset/ERR009097.bam
3511c8ba38f1f2f35410e61f06e0ef9c *inst/extdata/ERP000101_subset/ERR009097.bam.bai
729215eec8d154627a0b777f63454c70 *inst/extdata/ERP000101_subset/ERR009102.bam
421b7ed67628b45c8592b078092ff99b *inst/extdata/ERP000101_subset/ERR009102.bam.bai
78cbb9bd4c777bba46d9a50c3a32fbd6 *inst/extdata/ERP000101_subset/ERR009103.bam
a6b46426f1540d528b6e3ec00f1e5e4a *inst/extdata/ERP000101_subset/ERR009103.bam.bai
4e533548fd44323feacbfbb0c61fc1d4 *inst/extdata/ERP000101_subset/ERR009113.bam
32a48fbbfca74e7ead1417df31aec144 *inst/extdata/ERP000101_subset/ERR009113.bam.bai
920c5151e6bbcc171d506b5f94bd0dc3 *inst/extdata/ERP000101_subset/ERR009115.bam
df9370838aa0224da7315d562b0c1785 *inst/extdata/ERP000101_subset/ERR009115.bam.bai
e377aa5b075c4d6ce7d8d430f830e332 *inst/extdata/ERP000101_subset/ERR009122.bam
ffb10e3d379b61f40362a3d156809a14 *inst/extdata/ERP000101_subset/ERR009122.bam.bai
fbd0c8c945e9092789da91461a3bf35b *inst/extdata/ERP000101_subset/ERR009126.bam
fadc50f158eaa8b05413125f601142f5 *inst/extdata/ERP000101_subset/ERR009126.bam.bai
d3f1de716c0db380c0ada48f0427de7e *inst/extdata/ERP000101_subset/ERR009127.bam
c69625a4b58c88b3539f7281da1e2efa *inst/extdata/ERP000101_subset/ERR009127.bam.bai
dd1ae7a7e8e8af51b02535c231d3d5ff *inst/extdata/ERP000101_subset/ERR009129.bam
67cd6c305b2d57600332f077bc191c3b *inst/extdata/ERP000101_subset/ERR009129.bam.bai
06bc7a075f7be9b8e095aa48b811a58e *inst/extdata/ERP000101_subset/ERR009135.bam
bde4f256e5a288427b7b1e1e2cff5737 *inst/extdata/ERP000101_subset/ERR009135.bam.bai
71609e349dd469d210e5f46ba8380ebe *inst/extdata/ERP000101_subset/ERR009141.bam
758e75c1af1c0d32db68436cb7b6165c *inst/extdata/ERP000101_subset/ERR009141.bam.bai
7936cd1483442748d70307e4229198d2 *inst/extdata/ERP000101_subset/ERR009142.bam
cc60fb04474002a962494de9254ba732 *inst/extdata/ERP000101_subset/ERR009142.bam.bai
bc3163f8178d1f3d11e6b9076d1bbbff *inst/extdata/ERP000101_subset/ERR009144.bam
69dc97d75d37ffe24e376d56206e8b00 *inst/extdata/ERP000101_subset/ERR009144.bam.bai
54998a3d8851d198cbdc416ab34ffc0a *inst/extdata/ERP000101_subset/ERR009146.bam
d654f33b561ae33809acda14d302ca0b *inst/extdata/ERP000101_subset/ERR009146.bam.bai
dd26f0fa48c2a86d1f7d357b3b03682e *inst/extdata/ERP000101_subset/ERR009147.bam
1315b0aedd6ccc91d7a84ece7c11d5fb *inst/extdata/ERP000101_subset/ERR009147.bam.bai
0037cc10ccfee5d30f1c791ef18ef6fa *inst/extdata/ERP000101_subset/ERR009154.bam
2ee54b106be0700fd06f46294cb92b8e *inst/extdata/ERP000101_subset/ERR009154.bam.bai
d81735ee6936ff9ce4003eba9c5f034b *inst/extdata/ERP000101_subset/ERR009157.bam
758e75c1af1c0d32db68436cb7b6165c *inst/extdata/ERP000101_subset/ERR009157.bam.bai
938c9c6a62fb6e3efcb2b2c5fa45b922 *inst/extdata/ERP000101_subset/ERR009159.bam
e0ff4dfcaeae320b662c723c12bbeba3 *inst/extdata/ERP000101_subset/ERR009159.bam.bai
0d17dcc7bd2b6c7ac86e49e2d3531f3b *inst/extdata/ERP000101_subset/ERR009160.bam
ca8eb82634ff36d3f9d54894e4385540 *inst/extdata/ERP000101_subset/ERR009160.bam.bai
367da255056b3e8950f805e751ce23f2 *inst/extdata/ERP000101_subset/ERR009167.bam
a97bb003baae79c75d85b80d531fb315 *inst/extdata/ERP000101_subset/ERR009167.bam.bai
96f2e3fef8add1f76c4e3d9954e82ac8 *inst/extdata/hg19.chr17.subset.fa
b9b22df94054d14b3d7e88901be62ca1 *inst/extdata/hg19.chr17.subset.fa.fai
380180128db80692c7a85eb012a3e3aa *man/ASEset-barplot.Rd
f8c98e385359b05958840b07f022fb8d *man/ASEset-class.Rd
88a2f997d8e31a53cb17ac50665d1105 *man/ASEset-filters.Rd
aead5b1fa2e93372a9aff19d3a3daea7 *man/ASEset-gbarplot.Rd
739fd4a98a138515c0e15d5402a24611 *man/ASEset-glocationplot.Rd
598201b66e6ec1d2ce413ad9d3d166d5 *man/ASEset-gviztrack.Rd
9a44efa73e70a8bed69e9707eed98e3c *man/ASEset-scanForHeterozygotes.Rd
459a8a20b437650d0d369905879d513c *man/ASEset.old.Rd
4be85ff0e565bb843d955d84e79a40bb *man/ASEset.sim.Rd
279bcaebdd4b101f756f7f957e171486 *man/ASEsetFromBam.Rd
3eeb7b8490298a219dbd261ae6471753 *man/AllelicImbalance-package.Rd
5b95e786184cc8cdcf4d295fdfff7748 *man/DetectedAI-class.Rd
dafa0afd84807412ac1588b75e642e55 *man/DetectedAI-plot.Rd
64308a779a3d1a627f937666206a6c30 *man/DetectedAI-summary.Rd
23853508bc7bcf5a73ffc98a56614e1f *man/GRvariants.Rd
d0a62fac11d73e3b90190fbb906b2ce0 *man/GlobalAnalysis-class.Rd
42841ba955d0edaa25fd6a5318ef1761 *man/LinkVariantAlmlof-class.Rd
c54546037460587b4b33c9eb38584a57 *man/LinkVariantAlmlof-plot.Rd
5fc5d0c9ef848456e8110c101d1d6694 *man/RegionSummary-class.Rd
0cd5911d41af23374ae3444625f2183d *man/RiskVariant-class.Rd
3a701e69aaabaa8b0791fc2f089ab0a9 *man/annotation-wrappers.Rd
111e92fb51469ad8d22554a180861dd0 *man/annotationBarplot.Rd
1019df90f583c01d690ef32208063e95 *man/barplot-lattice-support.Rd
50666f7138983e8092ea44306bd13a37 *man/binom.test.Rd
801947b496bd3aba4e2b4bbf39fbaa57 *man/chisq.test.Rd
9d6d04adbbc52946cf0359498cbd6062 *man/cigar-utilities.Rd
33b91117ed91cec4fcc70ec15263cce6 *man/countAllelesFromBam.Rd
32e842957d63c2f59c54047aa48dc024 *man/coverageMatrixListFromGAL.Rd
4d2a29dc39a80c88de9426dc093418a4 *man/decorateWithExons.Rd
5d8b16599f057d7b68235d8770f5c0df *man/decorateWithGenes.Rd
46fa16e047c443b769b5cbb7ab56d17a *man/defaultMapBias.Rd
456788297db18811ffe321174a1e95ed *man/defaultPhase.Rd
31a0f55fe9c543fe14c978b347fccbd2 *man/detectAI.Rd
374ce8d43c98695d5b55218875e4a8b4 *man/fractionPlotDf.Rd
285b351b1f1ad1b0f4d844c5e6d15118 *man/gba.Rd
3f1f487ccf75d510bfc4ce4cc9449f2e *man/genomatrix.Rd
afb75c6afbf134b8bf212f5ebfd95d79 *man/genotype2phase.Rd
5b62d1f784eb1c15484792c924c7eae4 *man/getAlleleCounts.Rd
751a28bc143dea261feb6ddab43bb5f3 *man/getAlleleQuality.Rd
9b22e39d60be4d0e78418f02d8e0472e *man/getAreaFromGeneNames.Rd
5089467c28ae00366dec824aa69dadca *man/getDefaultMapBiasExpMean.Rd
30dc42ada9fcb7975ea9f0a68cf18ec4 *man/getSnpIdFromLocation.Rd
0a5e284f2797ee29aaae6ea4cff5ded8 *man/histplot.Rd
5c8693f0c6046938c18a82bb4c5cc044 *man/implodeList-old.Rd
a9f163c48088a5bd4beb782ebc5537bb *man/import-bam-2.Rd
5f4f864bf9e568f18fcb59f5f6ac9d56 *man/import-bam.Rd
58b9df842399d81a9d33304b8310926a *man/import-bcf.Rd
c35e5116d64fc26da38ebbc411d78733 *man/inferAlleles.Rd
4bbee3b8e4c76d2f006fb1ea74db22ba *man/inferAltAllele.Rd
d0cef1afa10e744e3808962dffcc14cc *man/inferGenotypes.Rd
a4a6f1ae6d3eba85ab8ea142bba521eb *man/initialize-ASEset.Rd
7cad490d8ed55e7a8a2eae3319f683dc *man/initialize-DetectedAI.Rd
21003e3b323538264971478ef7e158e2 *man/initialize-GlobalAnalysis.Rd
1716222b686abac271f2f2a2a15a7754 *man/initialize-RiskVariant.Rd
f2167df2383e81df13415d0e7edea61a *man/legendBarplot.Rd
24df8403359ab770fd11a2798f97be48 *man/locationplot.Rd
86254b3c85392c22698e4da54f13de39 *man/lva.Rd
0dc7b721a72965859663dfd42a30fc27 *man/lva.internal.Rd
5041c8d4c343f84bc50840df4f63368c *man/makeMaskedFasta.Rd
3e70c3fabfbdede04d0317690de49d77 *man/mapBiasRef.Rd
018d10c4fcc00d4f4986968e8488c808 *man/minCountFilt.Rd
b6fa6b48d0ce79a4dca2712b276158e3 *man/minFreqFilt.Rd
6a56517fb1b5d858eb06a35ea925df98 *man/multiAllelicFilt.Rd
57584a584491ee10bf5e5554ed0ed280 *man/phase2genotype.Rd
8eeb168c7a2b807e38d0954c08e0a112 *man/phaseArray2phaseMatrix.Rd
b695d1840e403f1addf3ec445e3df6ac *man/phaseMatrix2Array.Rd
7b303e76f6a73f3c940870e48184ac3a *man/randomRef.Rd
49c5f8921adc6cb92fd8cb7dcf49da08 *man/reads.Rd
4982e3cead61d7caf3a45781b340114e *man/refAllele.Rd
cb20525d035de55208d8316d977d8303 *man/regionSummary.Rd
3588c913f8b6da51b7a3b5f865fa0a24 *man/scanForHeterozygotes-old.Rd
554dacb14e73173ad353029140b1f1b7 *tests/test-all.R
6bffb3e59135caf32f04a6473d718273 *tests/testthat/test_calc_arank.R
3b8c67c7fd9c809170c6a8df7a509b10 *tests/testthat/test_calc_frequency.R
4ba8483134e5651363480d9dadb697c3 *tests/testthat/test_cigar_utility.R
ada610a0ba5320f4eaf66c3f9ba72c5f *tests/testthat/test_detectAI.R
0b33b8708e8827402e46da1967cef538 *tests/testthat/test_filters.R
500d4ae740f2fb76a3796b18e6e2f849 *tests/testthat/test_fraction.R
83b1f1b013d251c00f5f56ce10f3e92e *tests/testthat/test_frequency.R
cb9225cb334e0489adc4b8e514468648 *tests/testthat/test_genotype2phase.R
3e4eb177cd66c13fc54db39db3abee61 *tests/testthat/test_import_counts.R
06e277a0010a7015de89d0d611bfcfd7 *tests/testthat/test_infer_alleles.R
f26987a3554228ee0b49c54f7e8c4a7f *tests/testthat/test_infer_genotypes.R
52cfdb29d921686cc3dc66b2f71b47ad *tests/testthat/test_lva.R
3d4dc7d6b7d9d7400da3dcd7384ac06c *tests/testthat/test_phase.R
333602039ed0a26ac476909af61eda00 *tests/testthat/test_phase2genotype.R
3e7f33666411f4b8d14437ff8657b78f *tests/testthat/test_phaseArray2phaseMatrix.R
298bdcc9d9ac5ecebbca1303de03e488 *tests/testthat/test_refFraction.R
1bd713bbc598cd85367ab86ee553999e *tests/testthat/test_regionSummary.R
69e8f194e8b40720e4c5ac16a90e3187 *tests/testthat/test_utils.R
5e35b2e9a659f3dab6f8df1d5f3ce221 *vignettes/AllelicImbalance-vignette.Rmd
