f73bcdeabd462433ef7146822efd155a *DESCRIPTION
1958c40ab888a5586a03c80611f5a136 *NAMESPACE
130f55a3daa4e5ada21f45cc7a948667 *R/CheckAltReads.R
d6671512b6ac9b0e32f3cf86f499dcc4 *R/abemus.R
06a39c8b062b9639aa32d93ad57a8f5f *R/add_class.R
72b6a8e6da473a52f2aa23a7e012940e *R/add_class_xbg.R
dddc87d6a976641ad1a79d4387506aa3 *R/add_names.R
44cbb78d324009c844b687d59f5c3abd *R/adjust_af_threshold_table.R
9b75f44dd22ed04d254d49a17440df00 *R/apply_AF_filters.R
71b744ab2cb40cd617b358ba02ee89ff *R/apply_scaling_factor.R
cdc648ca5de26cd0ce7208a49d39e0d8 *R/bed2positions.R
32511ab343a4db7ae4edc54a6c00cfc0 *R/bombanel_afs.R
ae7e1389b38f8b0a093afe7bc24e17ac *R/bombanel_covs.R
7965f23731959c8fc30e9ee837e4ec21 *R/bombanel_tab_cov_pbem.R
ff7d71a4b9d7537402866aef71df457b *R/callsnvs.R
314e66d287bb8fb193968e9b3d86fa5e *R/compute_afthreshold.R
14eeb78ffd721f220f478309fb7c939a *R/compute_pbem.R
5f8012e382db2f87bca87f71c4117ffa *R/compute_pbem_allele.R
d8f60f3e1128a9ee47c06ea2cfb75796 *R/define_cov_bins.R
a23b4cc5cefe865582a431de99d293c5 *R/filter.R
b74ee2972ad246f672230be6ac2ece8c *R/fromListToDF.R
5e821b6a0a25cd046bfb9e78c4652ebb *R/get_afth.R
6084e4b4a7bb459ad82410263101e06f *R/get_case_mean_coverage.R
82700c2e64fd7f066585e0c84ed6352a *R/get_germlineset.R
4f49435a7f7ea3d86da479012a9e735a *R/get_pbem.R
998d2f6b0ce931430acf8f40104647f3 *R/get_stats_pbem.R
aeaaa3d5975783fb42b33ff3e4b4de93 *R/get_tabcalls_path.R
c9077b13fcd554ebad8eb78f2c20d779 *R/get_target_size.R
7dd13c9172441783cc780c5b29343bdc *R/import_sif.R
98c22427ae3c0d3dffa1071a4693be24 *R/pos2bperr.R
22a3c8d99868e33e45fcafb833248f6c *R/quantilezaf.R
dcd17a0a61eb4b28bb1eda476baaf5fc *R/split_pacbam_bychrom.R
cda175f1c6af3c4bd8464e77c57219cf *R/strandbias.R
5bb41b60b8599da78b84153fe51362ed *R/tab_optimal_R.R
3f25ed286460ec37e1380137942f6931 *README.md
30475933e20bec2970ec3cfbf74b10e8 *build/vignette.rds
fe19fb4c0610f17e2b70b873cf49985d *data/bombanel_afs.rda
3248a6a76d4e0d6f64466ee68f2d617d *data/bombanel_covs.rda
c35dfeef6c9ba66d624bea59e85b8972 *data/bombanel_tab_cov_pbem.rda
f55a5c38e1be95ffbc1884c3fcb02559 *data/datalist
3d82d60481440d431a41e714fd8df39d *data/tab_optimal_R.rda
09032cd3d4e98e42d7e62fe48749913d *inst/doc/abemus.Rmd
329435acc672887d759048457a2e10d9 *inst/doc/abemus.html
b8869ed01d3cfe75efd600b449f148fd *inst/extdata/BaseErrorModel/afgtz.tsv
b8869ed01d3cfe75efd600b449f148fd *inst/extdata/BaseErrorModel/afgtz_8.tsv
4211d29d4b06fb48318daba336e592c8 *inst/extdata/BaseErrorModel/afz.RData
b4ee5078272ecdf17ebc5929f205c69a *inst/extdata/BaseErrorModel/afz.tsv
b4ee5078272ecdf17ebc5929f205c69a *inst/extdata/BaseErrorModel/afz_8.tsv
6482f22be1fbc56af0b7fdafd0f91a15 *inst/extdata/BaseErrorModel/bperr.tsv
6482f22be1fbc56af0b7fdafd0f91a15 *inst/extdata/BaseErrorModel/bperr_8.tsv
200e6aa7329f767dc0e5c71344cd875f *inst/extdata/BaseErrorModel/bperr_summary.RData
0090692ca4598cef24bfa790cf0a1544 *inst/extdata/BaseErrorModel/pbem_background.RData
bbace22485b1a71c000910e1a0018e9e *inst/extdata/BaseErrorModel/pbem_tab.RData
6a7e3f9699b5a2194468a066bbd25dbd *inst/extdata/Controls/datathreshold.RData
0ba2924b0fc827c8e69a9f33c6a8515f *inst/extdata/Controls/minaf_cov_corrected_1r_0.995_b.RData
c7e5efffa6283694d4d7e76c71ed16ee *inst/extdata/Controls/tab1r_0.995_b.RData
38a63856d29ed6f9ae890f49f6be6fa2 *inst/extdata/Results/TUMOR_A_toy/8/chrpm_f1.tsv
c42bd8947cca799fd96e6aa31c1a0ede *inst/extdata/Results/TUMOR_A_toy/8/chrpm_f2.tsv
1d61552f9a9f6480be5395a0c146a081 *inst/extdata/Results/TUMOR_A_toy/8/chrpm_f3.tsv
2d9921b8dbc3fbc1fa3c1fd323f1eea6 *inst/extdata/Results/TUMOR_A_toy/pmtab_F1_TUMOR_A_toy.tsv
9f8625f3ee41936e6e384a363de9af5b *inst/extdata/Results/TUMOR_A_toy/pmtab_F2_TUMOR_A_toy.tsv
727ce5ba2cd3f9b135785d513cf67127 *inst/extdata/Results/TUMOR_A_toy/pmtab_F3_TUMOR_A_toy.tsv
0341d1d3440addae5c95f5e53b55c9ac *inst/extdata/Results/TUMOR_A_toy/pmtab_F3_optimalR_TUMOR_A_toy.tsv
c3f5272bef47ce230af1a751648e8b48 *inst/extdata/Results/filtering_criteria.txt
3044cd57011ed0ebd46d1300ab68b80b *inst/extdata/pacbam_data/CTRL_A_toy.pabs
d98c28f2f18468b381391f59fea873f5 *inst/extdata/pacbam_data/CTRL_A_toy.pileup
0c7affe965d1b61c59ddcac9821522a5 *inst/extdata/pacbam_data/TUMOR_A_toy.pabs
9af08210b80be937f61a918343316ca6 *inst/extdata/pacbam_data/TUMOR_A_toy.pileup
a19bbeae20f255d2215abac58e6c456a *inst/extdata/pacbam_data_bychrom/CTRL_A_toy/pileup/CTRL_A_toy_chr8.pileup
e4fb8db2509bbf3a30d6aa7aa347cfb3 *inst/extdata/pacbam_data_bychrom/CTRL_A_toy/snvs/CTRL_A_toy_chr8.pabs
9af08210b80be937f61a918343316ca6 *inst/extdata/pacbam_data_bychrom/TUMOR_A_toy/pileup/TUMOR_A_toy_chr8.pileup
0c7affe965d1b61c59ddcac9821522a5 *inst/extdata/pacbam_data_bychrom/TUMOR_A_toy/snvs/TUMOR_A_toy_chr8.pabs
d64d62a60f4dda0ceac0ea6dd61e7e84 *inst/extdata/regions_toy.bed
978a452fc5b852071f2a2b5f1b49e19e *inst/extdata/test_sif_toy.tsv
936ffd9f13a1cd202d1872d93cbcd438 *man/abemus.Rd
3120a8e5274a6e6197dc80123d8d66ae *man/apply_scaling_factor.Rd
9b71c0d8dc39a27d1ac50e66858e26c0 *man/bed2positions.Rd
2fd145a872fef75bab0bae00a40a7979 *man/bombanel_afs.Rd
810bf42d307260cdfeef7c450bca36ea *man/bombanel_covs.Rd
fb9db65649117d1b70b663c145941cdb *man/bombanel_tab_cov_pbem.Rd
b761395bea8fe16ed238a18adbb50770 *man/callsnvs.Rd
8991ba8116edf68ee6c74191a7806ff7 *man/compute_afthreshold.Rd
d73d000e01b49958d5f852878768923c *man/compute_pbem.Rd
c44fe615e9f2a9f456ca736cb493eba2 *man/get_case_mean_coverage.Rd
91e03318c491431fe52d805e228ac4f0 *man/get_target_size.Rd
46bc39ba8671d2ddcbe71f30b72c30b5 *man/split_pacbam_bychrom.Rd
b7ea26b0d1b12a034bb2943571138dcf *man/tab_optimal_R.Rd
09032cd3d4e98e42d7e62fe48749913d *vignettes/abemus.Rmd
