API for 6Youcai/ABSOLUTE
ABSOLUTE

Global functions
ABSOLUTE_comut_plot Source code
ABSOLUTE_mutation_VCF_matrix_plot Source code
ABS_class_mutsig Source code
ABS_mutsig_calc_and_plot Source code
AbsoluteResultPlot Source code
AllelicCalcChrArmDistr Source code
AllelicCalcClonalSSNVLoglik Source code
AllelicCalcGermlineSNVLoglik Source code
AllelicExtractSampleObs Source code
AllelicGetAbsSegDat Source code
AllelicGetCopyRatioComb Source code
AllelicGetMutSegIx Source code
AllelicMakeSegObj Source code
Allelic_get_seg_sigma Source code
AlphaBFunc Source code
AlphaFunc Source code
ApplyKaryotypeModel Source code
ApplySSNVModel Source code
Bernoulli_conv_pval Source code
CAPSEG_get_seg_sigma Source code
CalcAbDistr Source code
CalcDatLL Source code
CalcFitEntropy Source code
CalcModeLogCurv Source code
ClassifySamplesWgdByProfile Source code
ClassifySomaticVariants Source code
CollapseChrarmModelsToTcn Source code
CombLL Source code
CreateMutCnDat Source code
CreateReviewObject Source code
CrypticScnaPost Source code
DMultmix Source code
DP_loglik Source code
DP_mut_posterior_plots Source code
DP_post Source code
DP_post_K_plot Source code
DP_post_fixed Source code
DP_post_gamma_plot Source code
DP_prob_k_cond_gamma_N Source code
DetermineGroup Source code
DrawMutBetaDensities Source code
ExtractReviewedResults Source code
FilterSegs Source code
FindLocationModes Source code
FitPPModeSomaticMuts Source code
GenomeHetFilter Source code
GenomeHscrSegPlot Source code
GermlineMutPrior Source code
GetAllelicChrArmSegs Source code
GetAlphaAndTau Source code
GetCallStatus Source code
GetCentromerePos Source code
GetChrArmMat Source code
GetChrLens Source code
GetClustP Source code
GetCovForPow Source code
GetDatClustLL Source code
GetHscnGermlineMutComb Source code
GetHscnGermlineXMutComb Source code
GetHscnSomaticMutComb Source code
GetHscnSomaticXMutComb Source code
GetModeColors Source code
GetMutBetaDensities Source code
GetPpTabVals Source code
GetScnaPowTab Source code
GetScnaStderrGridDensity Source code
GetSegColsByAllelicBalance Source code
H_exp_subclonal_SSNV Source code
H_unif_subclonal_SSNV Source code
HapSeg_res_lookup Source code
Laplace_approx Source code
LogAdd Source code
MargModeFinder Source code
MatchPpMode Source code
MatchPpModes Source code
MultmixClustP Source code
Mut_AF_plot Source code
MyBarplot Source code
NegGenomeFilter Source code
PP_liftover_plot Source code
PlotFailedSamples Source code
PlotHscrAndSeghist Source code
PlotMode_review_summary Source code
PlotModes Source code
PlotModes_layout Source code
PlotModes_review_layout Source code
PlotSeglenHist Source code
PlotSomaticMutDensities Source code
PowerCalc Source code
PowerCalc_for_single_read Source code
PpModeScorerBarplot Source code
PrintFailedTable Source code
PrintPpCallTable Source code
ProvisionalModeSweep Source code
ReduceSegobjListToCalled Source code
ReorderModeRes Source code
RunAbsolute Source code
RunOpt Source code
SCNA_CCF_plot Source code
SCNA_SSNV_joint_posterior_CCF_plots Source code
SCNA_Theta_1d_opt_step Source code
SCNA_model_Theta_Laplace_approx Source code
SCNA_model_Theta_sweep_coord_ascent Source code
SCNA_model_Theta_tx Source code
SCNA_model_calc_Amp_LL Source code
SCNA_model_calc_CCF_DP_loglik Source code
SCNA_model_calc_log.clonal.seg.mat Source code
SCNA_model_calc_log.subclonal.seg.LL Source code
SCNA_model_clonal_seg_Q_post Source code
SCNA_model_eval_prior Source code
SCNA_model_init Source code
SCNA_model_loglik Source code
SCNA_model_opt_cond_b_delta Source code
SCNA_model_opt_mix.w Source code
SCNA_model_seg_mix.w_post Source code
SCNA_model_setup Source code
SIF_sample_query Source code
SLC_d_scaled_t Source code
SSNV_CCF_plot Source code
SSNV_FhatCombPost Source code
SSNV_on_subclonal_SCNA_CCF_plot Source code
S_inv_chisq_joint_MAP Source code
SelectMatchedModes Source code
Theta_LL_wrapper Source code
TotalCalcClonalSSNVLoglik Source code
WeighSampleModes Source code
WriteAbsSegtab Source code
aggregate_ABS_MAF_files Source code
aggregate_boolean_MAF_column Source code
aggregate_numeric_MAF_column Source code
aggregate_sample_MAF_list Source code
allelic_annotate_SSNVs_on_clonal_SCNAs Source code
allelic_calc_sample_muts_on_subclonal_scna Source code
allelic_eval_SNV_models_evidence Source code
allelic_get_cr_grid_from_ccf_grid Source code
allelic_get_muts_nearest_clonal_scna Source code
allelic_get_subclonal_SCNA_info Source code
allelic_get_subclonal_scna_mut_ix Source code
alt_get_perm_stirling_coefs Source code
annotate_SSNVs_on_subclonal_SCNAs Source code
apply_allelic_model_to_total_copy_ratios Source code
apply_review_and_extract Source code
assemble_ABSOLUTE_VCF_data Source code
batch_exec_ABSOLUTE Source code
build_gene_GR_data Source code
calc_CCF_95CI Source code
calc_SCNA_CCF_dens Source code
calc_SCNA_seg_mix_LL Source code
calc_SSNV_on_subclonal_SCNA_CCF_dens Source code
calc_ccf_posterior_LL_grid Source code
calc_ccf_posterior_dens_grid Source code
calc_ccf_summary Source code
calc_firstorder_subclonal_states Source code
calc_mode_seg_tabs Source code
calc_muts_ccf_postrior_LL_grid Source code
call_genome_wide_ABSOLUTE_SCNAs Source code
call_regions_ABSOLUTE_SCNAs Source code
called_detailed_SSNV_plots Source code
clonal_SSNV_Mult_Prior Source code
cluster_DP_loc_results Source code
cluster_prob Source code
comb_CDF Source code
comb_dens Source code
compute_cached Source code
compute_focality_score Source code
dDirichlet Source code
dPolya Source code
d_S_inv_chisq Source code
d_beta_binom Source code
d_igamma Source code
d_scaled_t Source code
deconstruct_SCNAs Source code
deconstruct_mode_results_SCNAs Source code
dens_PlotMode_review_summary Source code
detailed_SSNV_on_subclonal_HSCN_plot Source code
draw_grid_mut_densities Source code
draw_mut_multiplicity_densities Source code
eval_M_polynom Source code
extract_HAPSEG_segtab Source code
extract_total_copy_ratios_from_allelic_CAPSEG Source code
fill_mode.tab_row Source code
fill_mode_neighborhoods Source code
fillin.samps Source code
filter_sex_chromosomes Source code
firehose_CAPSEG_SIF Source code
fit_SSNV_model Source code
fit_modes_SCNA_models Source code
genotype_amp_and_del_SCNAs_in_called_ABS_files Source code
genotype_transcript_SCNAs_in_called_ABS_files Source code
get_GENCODE_transcript_GRs Source code
get_GISTIC_SCNA_genes Source code
get_MAF_list_from_called_seglist_obj Source code
get_SCNA_model_fit_plot_strings Source code
get_SCNA_thresholds Source code Source code
get_SSNV_on_clonal_CN_multiplicity_densities Source code
get_SSNV_on_subclonal_CN_multiplicity_densities Source code
get_SSNV_plot_colors Source code
get_TARGET_SCNA_genes Source code
get_all_annotated_reg_GRs Source code
get_allelic_abs_CN_seg_dat_from_allelic_CAPSEG_obj Source code
get_allelic_subclonal_scna_tab Source code
get_b_and_delta Source code
get_batch_args_from_SIF_with_HAPSEG_map Source code
get_clonal_seg_LL_mat Source code
get_cluster_stats Source code
get_comb_Wq0 Source code
get_comb_interval_gaussian_CDF_seg_mat Source code
get_gamma_prior_from_k_prior Source code
get_genome_coords Source code
get_grid_dens_95CI Source code
get_hap.q.keys Source code
get_hom_pairs_segtab Source code
get_hom_pairs_segtab_internal Source code
get_hom_seg_pair_map Source code
get_k_0_map Source code
get_log_cluster_stats Source code
get_log_stirling_coefs Source code
get_min_CCF_for_pow Source code
get_modal_chrarm_CN Source code
get_multi_VCF Source code
get_mut_cols Source code
get_mut_count_matrix Source code
get_neg_and_amp_Prs Source code
get_perm_stirling_coefs Source code
get_refgene_transcript_GRs Source code
get_sample_background_rate_convolved_event_significance Source code
get_seg_clust_tab Source code
get_seg_colors Source code
get_seg_mix_posts Source code
get_stirling_coefs Source code
get_subclonal_copy_states Source code
get_tcn_germline_X_mut_comb Source code
get_tcn_germline_mut_comb Source code
get_tcn_somatic_X_mut_comb Source code
get_tcn_somatic_mut_comb Source code
get_tcr_chr_arm_segs Source code
get_total_abs_CN_seg_dat_from_allelic_CAPSEG_obj Source code
get_total_subclonal_scna_tab Source code
get_variant_class_levels Source code
get_variant_classification_number Source code
grid_compose_LL Source code
homozygous_mutsig Source code
identify_potential_clinically_actionable_mutations Source code
init_DP_prior Source code
init_SSNV_model Source code
insert_default_args Source code
inv_softmax Source code
joint_SSNV_SCNA_grid_density Source code
load_GISTIC_peak_GR_data Source code
log_cluster_prob Source code
make_multi_VCF Source code
mode_SSNV_pow_calc Source code
modes_purity_ploidy_plot Source code
multiplicity_plot Source code
mut_qm_fc_grid_integral Source code
old_MatchPpMode Source code
old_get_cluster_stats Source code
old_run_diploid_snv_purity_opt Source code
old_tree_cluster_DP Source code
onLoad Source code
optimize_theta.Q Source code
orig_PowerCalc Source code
original_LogAdd Source code
original_call_genome_wide_ABSOLUTE_SCNAs Source code
original_genotype_transcript_SCNAs_in_called_ABS_files Source code
override_absolute_calls Source code
p_beta_binom Source code
p_scaled_t Source code
plot_ABS_comb_fit Source code
plot_ABS_seg_hist Source code
plot_SSNV_on_subclonal_SCNA_CCF_summaries Source code
plot_SSNVs_on_genome Source code
plot_mut_rates_and_sample_tracks Source code
plot_mutmat Source code
post_Dir_log_norm_const Source code
postprocess_seg_ancestral_and_derived_CN Source code
print_model Source code
prioritize_clinically_actionable_variants Source code
provisional_SCNA_LL Source code
rDirichlet Source code
reconcile_clonal_homdels_with_obs_SSNVs Source code
reduce_Phylogic_VCF Source code
reject_mutation_classes Source code
remove_empty_clusters Source code
resort_tree_clusters Source code
robust_summarize_DP_num_components Source code
run_1d_opt Source code
run_DP Source code
run_PP_calls_liftover Source code
run_diploid_snv_purity_opt Source code
run_seg_CCF_DP Source code
sample_gamma_cond_N_k Source code
sample_trans_ccf_plot Source code
scatter_jobs Source code
seg_SSNV_on_subclonal_SCNA_log_ev Source code
seg_focality_plots Source code
segs_in_comb_domain Source code
select_protein_change_annot_using_COSMIC Source code
select_samples_from_gene_SCNA_calls Source code
serial_dispatch Source code
set_allelic_funcs Source code
set_total_funcs Source code
simple_CAPSEG_SIF Source code
skip_seg_CCF_DP Source code
softmax Source code
sort_VCF_by_genemuts Source code
sum_marginalize_2D_sq_matrix Source code
sum_prior_on_2D_sq_matrix Source code
summarize_DP_num_components Source code
summarize_mut_locations Source code
summarize_predictive_density Source code
test_prior Source code
total_annotate_SSNVs_on_clonal_SCNAs Source code
total_calc_chr_arm_distr Source code
total_eval_SNV_models_evidence Source code
total_extract_sample_obs Source code
total_get_abs_seg_dat Source code
total_get_copy_ratio_comb Source code
total_get_cr_grid_from_ccf_grid Source code
total_get_mut_seg_ix Source code
total_get_muts_nearest_clonal_scna Source code
total_get_subclonal_SCNA_info Source code
total_get_subclonal_scna_mut_ix Source code
total_make_seg_obj Source code
tree_cluster_DP Source code
update_SSNV_mixture_weights Source code
weighted_sample_sd Source code
write_R_files Source code
write_called_seg_maf Source code
6Youcai/ABSOLUTE documentation built on June 10, 2017, 12:31 a.m.