2464e2f9081f8b578c31e066c360f5cd *CHANGES
c957bd346ed9b501957ed6de481443df *DESCRIPTION
770defa41aa4c8f3a2364d0fe193aa31 *NAMESPACE
70874a413f85e7c5fe1c194e57081eed *R/AllClasses.R
07a6c92dea0a16e1006767fa7236bf54 *R/AllGenerics.R
e7f9d9ca1ef8b4fa47c9a93f05194b45 *R/cnrma-functions.R
f70221d4b56bc803a40d31194d898d10 *R/cnset-accessors.R
0507ce20bfbb9e3555f29d12d0d64c35 *R/crlmm-functions.R
df24188f2b2553073a13c5bc73c92783 *R/crlmm-illumina.R
bd011c69c1aa9d7877ea8d99b6dc9186 *R/crlmmGT2.R
21d2cfa607d1ff71c86432ecd6167790 *R/krlmm.R
25dee0944dc982acf6bcac83b95456f7 *R/methods-AssayData.R
5a70497f876344a5a681af5ea8c942bb *R/methods-CNSet.R
73cfd5cccb3f36c3a0d4c65b83e7e50b *R/methods-CNSetLM.R
be63e23fd9d071d8faa266070cd6be26 *R/methods-PredictionRegion.R
0bab5c91452422ec3d0bb9f28b2fc0b5 *R/methods-SnpSuperSet.R
9e9418fe121f7211a4a9ab366a464d2a *R/methods-eSet.R
559654dc938d2a716aaf3d2a38e7985c *R/plot.R
17ffd76a64071e7c8c4088b857845282 *R/snprma-functions.R
d07fa9935f511f86cb98ab91a2fcea29 *R/test_crlmm_package.R
635feda42b67c1d59de3fb5a0e1ff854 *R/utils.R
c1e472a349a3071838c72d1ef8c0bf93 *R/zzz.R
8d92aa8d2aa4454205f7f0b11aebe1a5 *TODO
1cc7f769e3aebc3868bc0bf884fbc47d *build/vignette.rds
9eeed277f81a4b0d8be24e247f7dd0e8 *data/cnSetExample.rda
133d3d041ed4cf81736b748e8403b569 *data/cnSetExample2.rda
2215526415fcb853a1740c6eae3cde4d *data/datalist
de8bd39fbcd0f69450c8614bdeea6db1 *inst/CITATION
52c2b443af67b18a9a1d43e4a5b364fa *inst/NEWS.Rd
1a44540e3cd855839ceaae01c9880eff *inst/doc/AffyGW.Rnw
6b0e9879e07aa1f8f1b4c122b74eec3b *inst/doc/AffyGW.pdf
bfb3954a21506fb1d0e38de1b741783a *inst/doc/CopyNumberOverview.Rnw
dc7dc5d0fe2f45b4d963ca3e1e448932 *inst/doc/CopyNumberOverview.pdf
3bc53551ccd8b20fed5a6728d7444967 *inst/doc/IlluminaPreprocessCN.Rnw
bb8c3468e29e2832ba98d92e74840017 *inst/doc/IlluminaPreprocessCN.pdf
c9647c2e113f63e27fa6685660a05950 *inst/doc/Infrastructure.Rnw
8ac5123529470981c97f11c192939841 *inst/doc/Infrastructure.pdf
a7ca79be823d472eeaf74419b673e711 *inst/doc/genotyping.R
8c1d8f0adb7d713a08de5f76534ab328 *inst/doc/genotyping.Rnw
f0cd9af04f19b64d3ed03076bf6b8fcf *inst/doc/genotyping.pdf
15e6c6521613b6fb1ffc81e1ef27b136 *inst/doc/gtypeDownstream.Rnw
53b2d334953694adf148373b12141100 *inst/doc/gtypeDownstream.pdf
f168940373abbc661802c820da47bb5b *inst/scripts/AffyGW.Rnw
6b0e9879e07aa1f8f1b4c122b74eec3b *inst/scripts/AffyGW.pdf
247f3470274fd2660c6a6bce933c9252 *inst/scripts/IlluminaPreprocessCN.Rnw
bb8c3468e29e2832ba98d92e74840017 *inst/scripts/IlluminaPreprocessCN.pdf
a23404272fd2e025eeb10b45158076d1 *inst/scripts/Infrastructure.Rnw
8ac5123529470981c97f11c192939841 *inst/scripts/Infrastructure.pdf
274d824aa4a1370220226abcb21f8e19 *inst/scripts/Makefile
73d220246cc1175ff869b4d788891412 *inst/scripts/copynumber.Rnw
987109a365acbbc9603caecb9d5bc1e7 *inst/scripts/crlmmDownstream.pdf
daf61631368c89a22836c4651097edbf *inst/scripts/crlmmIllumina.Rnw
122bb614388d653ac1855fcf2b2b8ed9 *inst/scripts/crlmmIllumina.pdf
2de2109c1186126d6da2da5c7047b9ca *inst/scripts/gtypeDownstream.Rnw
53b2d334953694adf148373b12141100 *inst/scripts/gtypeDownstream.pdf
2e8c9696770488cc651a918fe485c9b1 *inst/scripts/refs.bib
d8114badf5209b2057a44598d7e8c6f9 *inst/scripts/sync
0beb6d7965143bff9dd7d7590e084dc3 *inst/unitTests/Makefile
70b613009b7f033e26a7dc34f49bacfc *inst/unitTests/test_crlmm.R
257a20a0dd416f03d64bc4638f275a29 *inst/unitTests/test_dataExamples.R
4d8054a423aa7fbdd84ca8bd56423bcb *inst/unitTests/test_ff.R
f9827e27e8ba7dadafaff79403a2b5f8 *man/ABpanel.Rd
58ff5eb37551511328a59b78f4cc9023 *man/AssayData-methods.Rd
fada4535676a8275e484f55fb434fbca *man/CNSet-methods.Rd
123a56bab2b96e2b031b6b161b152ef3 *man/ListClassConstructors.Rd
14f9868cfccc8491b39d5784ad59ae9e *man/PredictionRegion-class.Rd
47bdcbd1ece6a98300e95d119c532b9c *man/batchStatisticAccessors.Rd
92c8c6b35b21bbaf54385b861c548774 *man/calculateRBaf.Rd
5a2690116e11b64e28613957b8f6e00d *man/celfile-utils.Rd
c1c710dd5c7e49da23cc7c0c004682fd *man/cnSetExample.Rd
07bec3fb4ddc2a3e37bc61254b95b163 *man/cnrmaAffy.Rd
552a9291fc3448b7e93cc7e35827c105 *man/constructAffyCNSet.Rd
55e3b98002545242e3bcccfb771fe5a2 *man/constructInf.Rd
2cf38bee63fbbe2613bf41d2d348a26f *man/copynumberAccessors.Rd
3d87ab79ec3148e8dcecca69d56b7609 *man/crlmm-package.Rd
534eaba85c12203fc6d51de83e8ae4bf *man/crlmm.Rd
6cbc01503e2b48da994f2b074b9de3a7 *man/crlmmCopynumber.Rd
a0514ac7ce153f6927468fefd0e9488e *man/genotype.Illumina.Rd
9b41bf70f26851cd1e88653cf40bd578 *man/genotype.Rd
1548d18047f2114af7141c36f9c3b618 *man/genotypeAffy.Rd
470ed959603acfa2ffbbf8a1d45c9179 *man/genotypeInf.Rd
b6f24a69ed7e9f326f16c587b925158d *man/genotypes.Rd
5b83f5d607b4217b6a95ab414bf944fa *man/plotSNPs.Rd
85c26b152293ffc413398dd2cd9b84b8 *man/posteriorProbability.Rd
5e37227a42bc1e1eebad0a8c619880ff *man/predictionRegion.Rd
d44c977dccd839dd1159636f9f9cec77 *man/preprocessInf.Rd
c6e1964bdb1f234b730b453bb61e4763 *man/readGenCallOutput.Rd
749742f1b07d59cbe0ee42ae6080c5f3 *man/readIdatFiles.Rd
a747ba5c3f8c3da678561565512da2eb *man/snprma.Rd
d15ef443a63cebb69e3c48e266aed704 *man/snprmaAffy.Rd
5fdada4f72854fe0ac119cecf0a56fc5 *man/validCdfNames.Rd
a0303ac2ec5cfb6944afeb86f550c06a *man/xyplot.Rd
e63279bc67f1eb4cfe5b83aeb750f321 *src/crlmm.h
c334560e71775bf803f662cc3e66b099 *src/gtypeCaller.c
1bb918feb1f96240454f80b813378a1b *src/init.c
182a4ee66a538d00564bf76be374967f *src/trimmed.c
99ff61045644ced2e3624ad22c80fa80 *src/utils.c
fb5d979f0b25b2227a333363bb4061c5 *src/utils.h
18d20ca56451e6fb6151cb6408619eca *tests/crlmm_unit_tests.R
05fd52a826dbaa5afbf62247904bb931 *tests/doRUnit.R
1a44540e3cd855839ceaae01c9880eff *vignettes/AffyGW.Rnw
bfb3954a21506fb1d0e38de1b741783a *vignettes/CopyNumberOverview.Rnw
3bc53551ccd8b20fed5a6728d7444967 *vignettes/IlluminaPreprocessCN.Rnw
c9647c2e113f63e27fa6685660a05950 *vignettes/Infrastructure.Rnw
8f3ed1973d4a710605b57d6c7727b6f9 *vignettes/Makefile
122bb614388d653ac1855fcf2b2b8ed9 *vignettes/crlmmIllumina.pdf
8c1d8f0adb7d713a08de5f76534ab328 *vignettes/genotyping.Rnw
15e6c6521613b6fb1ffc81e1ef27b136 *vignettes/gtypeDownstream.Rnw
