3fd587b17cec827cf3c7036df25c5353 *DESCRIPTION
5f76fbc91b221820ccb851813a2ce594 *NAMESPACE
d4545d162050a329d27c1dc95217bab8 *NEWS
e8e355e4ed2454f222d451b9387f9516 *R/bam_qc_calc.r
f75eb55050c3cfdea28e5e039b3ee3ba *R/bam_qc_plot.r
d93773085cab93f3bd7cdc30c1ff115e *R/getByLocation.r
07fa33d9d7a3ce754d43e6506257c57d *R/param.r
dbfc3147d974058e3355eeb9fb6ac1a3 *R/plotting.r
6c58f938e53f2f1df9bed5c6f31f4181 *R/ramwas.r
8e1d43b6e6127426da127b17dfb98c6e *R/rowcolSumSq.r
6df37169a2c702008ff2066ca1c1f762 *R/rw0simdata.r
858344ce54f5f6864c32de483c3eefb6 *R/rw1scanBam.r
1c8f218aba622b90786a5218286fa649 *R/rw2collectqc.r
d4ccab1533191155477d5ce6a99e3208 *R/rw3covMatrix.r
e5aa21c38f01ce347d6003306c02150c *R/rw4pca.r
13d22f248d2e3db6418b268ece5e6f88 *R/rw5mwas.r
72b0f28faab54f1bfa4905c1245482e5 *R/rw6anno.r
736e372c192e5512ed262cfeff3a65ad *R/rw7mmcv.r
ca77f8e68c4952e289badf6f23a55676 *R/rwCellTypeEst.r
5e1c16717da8e38fd2a473028350df6c *R/rwCpGset.r
e4ca9e35ddaf0851c0a19109ff525b98 *R/rwDataClass.r
f436ab62ce67a2be6983fe7c57c5b576 *R/rwDataSubset.r
a4ae3e8d5bc8aa8a351f419f645a0600 *R/rwSNPS.r
31cb6fb4c460396649430853a455916e *build/vignette.rds
67b62f98911c27f6e0badd50f5763b30 *inst/CITATION
1adc2de8fb31721bc0e57eb0225e002c *inst/doc/RW1_intro.R
b1e2e722c8d4c23c752ae5aab2d9174d *inst/doc/RW1_intro.Rmd
a32a0bb1c41cf29771a0fb1d442074c4 *inst/doc/RW1_intro.html
81043817aea145f6177d8803ea38a8ba *inst/doc/RW2_CpG_sets.R
8357085dd4fa6c7136cd4abd1594bc89 *inst/doc/RW2_CpG_sets.Rmd
f57a82b2b1ae6e33e5c7286a5835c9f3 *inst/doc/RW2_CpG_sets.html
6312df7d55eba8062666daad28220ecd *inst/doc/RW3_BAM_QCs.R
5e0e1563bcdffdd0db8e722575193611 *inst/doc/RW3_BAM_QCs.Rmd
4de7faa51cba47f779e018d586471f09 *inst/doc/RW3_BAM_QCs.html
caa220bc17a19f74dd748c99e66ae0a2 *inst/doc/RW4_SNPs.R
7650c7c87bbc87195ac866a809aa8322 *inst/doc/RW4_SNPs.Rmd
37ead10542b3fd64ad33436311b0df54 *inst/doc/RW4_SNPs.html
757b2ca4c04fa641cafd9c7d466e33f7 *inst/doc/RW5a_matrix.R
eb1c6a2227b0d5556d0f5598429febaa *inst/doc/RW5a_matrix.Rmd
d819b0df3285b9ad2ae3890f5aa5b36e *inst/doc/RW5a_matrix.html
3cd5038723415d6e6d6965a0bc17c5a6 *inst/doc/RW5c_matrix.R
2c87427ae4ecf628238ab105145c1ece *inst/doc/RW5c_matrix.Rmd
e7de85e13162dbbe670905cdd38d7533 *inst/doc/RW5c_matrix.html
4711b7be6011c1aafe89aedfd04b4ad5 *inst/doc/RW6_param.R
88d9858ab7d60f741b011e2847efe392 *inst/doc/RW6_param.Rmd
2ef20aaa3b8495d7187afa88930ba1ef *inst/doc/RW6_param.html
daac74d5592340cb4d0a7c1767dcda03 *inst/extdata/bigQC.rds
00024093426229e222538fcb183ce311 *inst/extdata/cpgset.rds
e237a430f5a97c7c232eabcc64683e48 *inst/extdata/param_file.txt
0c64916b100bc58b26e5760945ba4af8 *inst/extdata/qc_sample.rds
fc8195b250f14110a5ef158e9bc0020f *inst/extdata/small.bam
b276fbbabc6ce70e3e43390e8fdf0b0e *man/MakeBED.Rd
9df14da6d6c58692b1911b052f49e68a *man/QCs.Rd
40409378b2273364fbc338ee198ddf46 *man/RaMWAS.Rd
5d87c676d01f7d87fbd0072f4632ce71 *man/cachedRDSload.Rd
0992f9a79f97864744cc39ff2b1d72c9 *man/figures/hint.png
291e826e767789679bdb7e65417b3b9d *man/findBestNpvs.Rd
f89410be95450f9ac25641d63e031f21 *man/get.Rd
14329d4e83e37f0e4383d4f302fda795 *man/getCpGset.Rd
e17ad6c2d24e5617ebbae4588f077033 *man/injectSNPsMAF.Rd
6550631cba56772767a6ad4fff182c66 *man/insilicoFASTQ.Rd
e29f275ae849cf6e9ce74ba9c82d2c2e *man/isAbsolutePath.Rd
a56a5e64c8661e42ee5d07bdd6cf58b0 *man/makefullpath.Rd
282040e21c3b1c55b791bf61bc63758b *man/manhattan.Rd
2af57a271037c78c0a92be985e4f01f6 *man/mat2cols.Rd
ca61758c2b11798f1d5dd651b5d3315a *man/orthonormalizeCovariates.Rd
2f7affa897033eed3dba771f31209350 *man/parameterDump.Rd
96434022056ac0c9961629ef3fdbd780 *man/parameterPreprocess.Rd
b0d19275813810a9d54b68b8ac1335a2 *man/parametersFromFile.Rd
ea69b2ecdbb9890b0bee9065f8154e3e *man/pipeline.Rd
b610f828fe0a51fbfea69746fff28f70 *man/plotCV.Rd
18442b07d1a71d72bde86740c6e2a5db *man/plotFragmentSizeDistributionEstimate.Rd
7a392fdf694a1534fb33eebc8c9e70b2 *man/plotPC.Rd
1c71c52318155fa9c0031564a0843ad4 *man/processCommandLine.Rd
b6fbcdc1b8e212cdb8faeb62abcea278 *man/pvalue2qvalue.Rd
74fa3b9b10a4bb81b53b04acf70c4c40 *man/qqplotFast.Rd
7d2827536160755eabefdc12852b9c31 *man/ramwas0createArtificialData.Rd
91b6eb2e610f574b481ccc47d6f9b010 *man/ramwasAnnotateLocations.Rd
f686f5a42879b46e4a88de23ca9b129c *man/ramwasParameters.Rd
645fef17a6cffa68ed882a449304e8b6 *man/rowcolSumSq.Rd
ad2774667d4059ed921060089c2b9108 *man/rwDataClass-class.Rd
f6b2252c2176dc861e59972b5f67da86 *man/subsetData.Rd
8c4d085e176d094ad6a1f43119ed6d72 *man/testPhenotype.Rd
1f3ed0ef6308606d9f6b5d3178ed055d *src/rw_c_code.c
21d091c493edee3e578d19c85b2e1f4b *vignettes/Flow.png
c313d576c4fab31b6f883b117a480cf7 *vignettes/PCval.png
4ba58805b9ff93c7d49a0266df8a0feb *vignettes/PCvec.png
ca8b0725c70df060777283c1cd992770 *vignettes/QQfull.png
fd36a4a15c66e826d0c7edc4c49a9270 *vignettes/QQnull.png
b1e2e722c8d4c23c752ae5aab2d9174d *vignettes/RW1_intro.Rmd
8357085dd4fa6c7136cd4abd1594bc89 *vignettes/RW2_CpG_sets.Rmd
5e0e1563bcdffdd0db8e722575193611 *vignettes/RW3_BAM_QCs.Rmd
7650c7c87bbc87195ac866a809aa8322 *vignettes/RW4_SNPs.Rmd
eb1c6a2227b0d5556d0f5598429febaa *vignettes/RW5a_matrix.Rmd
2c87427ae4ecf628238ab105145c1ece *vignettes/RW5c_matrix.Rmd
88d9858ab7d60f741b011e2847efe392 *vignettes/RW6_param.Rmd
dd2018d35a69a0573554b4b0af5e8daf *vignettes/bib.bib
