hapROH
latest
Contents:
Overview
Installation
hapROH
hapCon
hapCon_ROH
Frequently Asked Questions (FAQ)
API Reference
hapROH
Index
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Index
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C
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D
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A
ad_to_gentoypeL() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
add_gt_data() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
apply_error() (hapsburg.PackagesSupport.simData.Simulator method)
B
bam2hdf5() (in module hapsburg.PackagesSupport.loadEigenstrat.saveHDF5)
bam_to_hdf5() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
bamTable2hdf5() (in module hapsburg.PackagesSupport.loadEigenstrat.saveHDF5)
base_path (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad attribute)
bin_width (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
BinomSim (class in hapsburg.PackagesSupport.simData)
BinomSimCopyBoth (class in hapsburg.PackagesSupport.simData)
BinomSimRefNoLD (class in hapsburg.PackagesSupport.simData)
block_shr_density() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
bring_over_samples() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
C
c (hapsburg.emissions.RC_Model_Emissions_withContamination attribute)
calc_average_roh() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
calc_posterior() (hapsburg.hmm_inference.HMM_Analyze method)
calc_posterior_lowmem() (hapsburg.hmm_inference.HMM_Analyze method)
calc_transitions() (hapsburg.transitions.Model_Transitions method)
(hapsburg.transitions.Transitions method)
calculate_full_bin_prob() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
calculate_thr_shr() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
calculate_trans_mat() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
call_roh() (hapsburg.postprocessing.PostProcessing method)
ch (hapsburg.hmm_inference.HMM_Analyze attribute)
(hapsburg.preprocessing.PreProcessing attribute)
chr_lgts (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
(hapsburg.PackagesSupport.roh_expectations.Expected_Roh attribute)
chrom_length() (in module hapsburg.figures.plot_individual_roh)
ci_li() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
clean_up() (hapsburg.postprocessing.PostProcessing method)
coal_prob() (in module hapsburg.figures.plot_individual_roh)
coal_prob_rel() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
combine_hdf5s() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
combine_individual_data() (in module hapsburg.PackagesSupport.parallel_runs.helper_functions)
combine_ROH_df() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
compute_tot_neg_likelihood() (hapsburg.hmm_inference.HMM_Analyze method)
compute_tot_neg_likelihood_2d() (hapsburg.hmm_inference.HMM_Analyze method)
concat_fields() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
conPop (hapsburg.preprocessing.PreProcessingHDF5 attribute)
copyHaplo() (hapsburg.PackagesSupport.simData.BinomSim method)
(hapsburg.PackagesSupport.simData.BinomSimCopyBoth method)
(hapsburg.PackagesSupport.simData.Simulator method)
cov_dist (hapsburg.PackagesSupport.simData.MultiVariateNormalLD attribute)
create_bins() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
create_combined_ROH_df() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
create_cousins_roh() (in module hapsburg.figures.plot_bars)
create_df() (hapsburg.postprocessing.PostProcessing method)
(hapsburg.postprocessing.PostProcessingX method)
create_folders() (in module hapsburg.PackagesSupport.parallel_runs.helper_functions)
create_ne_dct() (in module hapsburg.figures.plot_ibdx)
create_Ne_roh() (in module hapsburg.figures.plot_bars)
create_Ne_roh_nr() (in module hapsburg.figures.plot_ibdx)
cutoff_post (hapsburg.postprocessing.PostProcessing attribute)
D
density_fun (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
destroy_phase_func() (hapsburg.preprocessing.PreProcessingHDF5 method)
df_snp (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad attribute)
Diploid_GT_Emissions (class in hapsburg.emissions)
diploid_ref (hapsburg.preprocessing.PreProcessingHDF5 attribute)
downsample (hapsburg.preprocessing.PreProcessingHDF5 attribute)
E
e_mat (hapsburg.emissions.Diploid_GT_Emissions attribute)
(hapsburg.emissions.Model_Emissions attribute)
(hapsburg.emissions.RC_Model_Emissions attribute)
e_model (hapsburg.hmm_inference.HMM_Analyze attribute)
e_rate (hapsburg.emissions.Diploid_GT_Emissions attribute)
(hapsburg.emissions.Model_Emissions attribute)
(hapsburg.emissions.RC_Model_Emissions attribute)
e_rate_ref (hapsburg.emissions.Diploid_GT_Emissions attribute)
(hapsburg.emissions.RC_Model_Emissions attribute)
eigenstrat_to_hdf5() (in module hapsburg.PackagesSupport.loadEigenstrat.saveHDF5)
EigenstratLoad (class in hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat)
EigenstratLoadUnpacked (class in hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat)
emission_matrix (hapsburg.emissions.RC_Model_Emissions_withContamination attribute)
Emissions (class in hapsburg.emissions)
end (hapsburg.hmm_inference.HMM_Analyze attribute)
error_model (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
error_model() (hapsburg.PackagesSupport.simData.Simulator method)
es (in module hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat)
es_get_index_iid() (hapsburg.preprocessing.PreProcessingEigenstrat method)
(hapsburg.preprocessing.PreProcessingEigenstratX method)
estimates (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
excluded (hapsburg.preprocessing.PreProcessingHDF5 attribute)
exp_blocks_full_individual() (in module hapsburg.figures.plot_individual_roh)
exp_roh_ind_rel() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
exp_roh_len_in_bin_N() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
exp_roh_len_in_bin_rel() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
expected_block_pdf() (in module hapsburg.figures.plot_individual_roh)
expected_block_pdf_chromosomes() (in module hapsburg.figures.plot_individual_roh)
Expected_Roh (class in hapsburg.PackagesSupport.roh_expectations)
exponentiate_r() (in module hapsburg.hmm_inference)
extract_df_age() (in module hapsburg.figures.plot_timelines)
(in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
extract_df_geo() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
extract_pop() (in module hapsburg.figures.plot_timelines)
extract_rc_hdf5() (hapsburg.preprocessing.PreProcessingHDF5 method)
extract_rmap_hdf5() (hapsburg.preprocessing.PreProcessingHDF5 method)
extract_snps() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
extract_snps_contaminationPop() (hapsburg.preprocessing.PreProcessingHDF5 method)
extract_snps_es() (hapsburg.preprocessing.PreProcessingEigenstrat method)
(hapsburg.preprocessing.PreProcessingEigenstratX method)
extract_snps_hdf5() (hapsburg.preprocessing.PreProcessingHDF5 method)
extract_snps_hdf5_lowmem() (hapsburg.preprocessing.PreProcessingHDF5_lowmem method)
extract_sub_df_geo_kw() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
F
first_state() (hapsburg.PackagesSupport.simData.BinomSim method)
fit() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
fit_gp() (in module hapsburg.figures.plot_timelines)
fit_ll_profile() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
flipstrand (hapsburg.preprocessing.PreProcessingEigenstrat attribute)
(hapsburg.preprocessing.PreProcessingEigenstratX attribute)
(hapsburg.preprocessing.PreProcessingHDF5 attribute)
folder (hapsburg.hmm_inference.HMM_Analyze attribute)
(hapsburg.postprocessing.PostProcessing attribute)
(in module hapsburg.postprocessing)
folder_out (hapsburg.preprocessing.PreProcessingHDF5 attribute)
fp_rate (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
full_shr_pr (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
fwd_bkwd (hapsburg.hmm_inference.HMM_Analyze attribute)
fwd_bkwd_p() (in module hapsburg.func)
G
get_1000G_path() (hapsburg.preprocessing.PreProcessingEigenstrat method)
(hapsburg.preprocessing.PreProcessingEigenstratX method)
get_bl_shr_interval() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
get_ci_counts() (in module hapsburg.figures.plot_ibdx)
get_default_res() (in module hapsburg.PackagesSupport.fit_ne)
get_enc_index() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
get_geno_all() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
get_geno_i() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
(hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoadUnpacked method)
get_geno_indvidiaul_iid() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
get_IBD_stats() (in module hapsburg.figures.plot_ibdx)
get_IBD_stats_pops() (in module hapsburg.figures.plot_ibdx)
get_index_iid() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
(hapsburg.preprocessing.PreProcessingHDF5 method)
get_index_iid_legacy() (hapsburg.preprocessing.PreProcessingHDF5 method)
get_post_processed_df() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
get_ref_ids() (hapsburg.preprocessing.PreProcessingEigenstrat method)
(hapsburg.preprocessing.PreProcessingHDF5 method)
get_segment() (hapsburg.preprocessing.PreProcessingHDF5 method)
get_sep_from_extension() (in module hapsburg.PackagesSupport.parallel_runs.helper_functions)
get_summ_as_df() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
get_transform() (hapsburg.PackagesSupport.sqrt_scale.SquareRootScale method)
give_bit_file() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
give_df_clsts() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
give_emission() (hapsburg.emissions.Diploid_GT_Emissions method)
(hapsburg.emissions.Model_Emissions method)
(hapsburg.emissions.RC_Model_Emissions method)
(hapsburg.emissions.RC_Model_Emissions_withContamination method)
give_emission_matrix() (hapsburg.emissions.Emissions method)
(hapsburg.emissions.Model_Emissions method)
(hapsburg.emissions.RC_Model_Emissions method)
(hapsburg.emissions.RC_Model_Emissions_withContamination method)
give_emission_state() (hapsburg.emissions.Diploid_GT_Emissions method)
(hapsburg.emissions.Emissions method)
(hapsburg.emissions.Model_Emissions method)
(hapsburg.emissions.RC_Model_Emissions method)
(hapsburg.emissions.RC_Model_Emissions_withContamination method)
give_iid_paths() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
give_pair_iids() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
give_positions() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
give_ref_alt() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
give_stats_cm_bin() (in module hapsburg.figures.plot_ibdx)
give_sub_df() (in module hapsburg.figures.plot_ibdx)
give_transitions() (hapsburg.transitions.Model_Transitions method)
(hapsburg.transitions.Transitions method)
gl_to_pl() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
H
h (hapsburg.PackagesSupport.simData.BinomSimRefNoLD attribute)
h5_path1000g (hapsburg.preprocessing.PreProcessingEigenstrat attribute)
(hapsburg.preprocessing.PreProcessingEigenstratX attribute)
(hapsburg.preprocessing.PreProcessingHDF5 attribute)
(hapsburg.preprocessing.PreProcessingHDF5Sim attribute)
hapCon_chrom_BFGS() (in module hapsburg.PackagesSupport.hapsburg_run)
hapCon_chrom_BFGS_legacy() (in module hapsburg.PackagesSupport.hapsburg_run)
haps (hapsburg.PackagesSupport.simData.SimRef attribute)
hapsb_chrom() (in module hapsburg.PackagesSupport.hapsburg_run)
hapsb_chrom_lowmem() (in module hapsburg.PackagesSupport.hapsburg_run)
hapsb_chromXs() (in module hapsburg.PackagesSupport.hapsburg_run)
hapsb_chunk_negloglik_preload() (in module hapsburg.PackagesSupport.hapsburg_run)
hapsb_femaleROHcontam_preload() (in module hapsburg.PackagesSupport.hapsburg_run)
hapsb_ind() (in module hapsburg.PackagesSupport.hapsburg_run)
hapsb_multiChunk_preload() (in module hapsburg.PackagesSupport.hapsburg_run)
hapsburg
module
hapsburg.emissions
module
hapsburg.figures
module
hapsburg.figures.plot_bars
module
hapsburg.figures.plot_ibdx
module
hapsburg.figures.plot_individual_roh
module
hapsburg.figures.plot_posterior
module
hapsburg.figures.plot_timelines
module
hapsburg.func
module
hapsburg.hapCon_ROH
module
hapsburg.hapCONX
module
hapsburg.hmm_inference
module
hapsburg.PackagesSupport
module
hapsburg.PackagesSupport.fit_ne
module
hapsburg.PackagesSupport.h5_python
module
hapsburg.PackagesSupport.h5_python.h5_functions
module
hapsburg.PackagesSupport.hapsburg_run
module
hapsburg.PackagesSupport.loadEigenstrat
module
hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat
module
hapsburg.PackagesSupport.loadEigenstrat.saveHDF5
module
hapsburg.PackagesSupport.parallel_runs
module
hapsburg.PackagesSupport.parallel_runs.helper_functions
module
hapsburg.PackagesSupport.pp_individual_roh_csvs
module
hapsburg.PackagesSupport.roh_expectations
module
hapsburg.PackagesSupport.simData
module
hapsburg.PackagesSupport.sqrt_scale
module
hapsburg.postprocessing
module
hapsburg.preprocessing
module
hapsburg.transitions
module
hdf5_to_vcf() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
HMM_Analyze (class in hapsburg.hmm_inference)
I
iid (hapsburg.hmm_inference.HMM_Analyze attribute)
(hapsburg.preprocessing.PreProcessing attribute)
ind_roh_from_pdf() (in module hapsburg.PackagesSupport.fit_ne)
individual_roh_statistic() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
inds_roh_from_pdf() (in module hapsburg.PackagesSupport.fit_ne)
initialize_ll_model() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
input_dims (hapsburg.PackagesSupport.sqrt_scale.SquareRootScale.InvertedSquareRootTransform attribute)
(hapsburg.PackagesSupport.sqrt_scale.SquareRootScale.SquareRootTransform attribute)
inverted() (hapsburg.PackagesSupport.sqrt_scale.SquareRootScale.InvertedSquareRootTransform method)
(hapsburg.PackagesSupport.sqrt_scale.SquareRootScale.SquareRootTransform method)
is_binary_file() (in module hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat)
is_separable (hapsburg.PackagesSupport.sqrt_scale.SquareRootScale.InvertedSquareRootTransform attribute)
(hapsburg.PackagesSupport.sqrt_scale.SquareRootScale.SquareRootTransform attribute)
J
jump_no_roh() (hapsburg.PackagesSupport.simData.BinomSim method)
jump_roh() (hapsburg.PackagesSupport.simData.BinomSim method)
(hapsburg.PackagesSupport.simData.BinomSimCopyBoth method)
K
k (hapsburg.PackagesSupport.simData.BinomSimRefNoLD attribute)
(hapsburg.PackagesSupport.simData.MultiVariateNormalLD attribute)
L
l (hapsburg.PackagesSupport.simData.BinomSimRefNoLD attribute)
(hapsburg.PackagesSupport.simData.MultiVariateNormalLD attribute)
(hapsburg.PackagesSupport.simData.Simulator attribute)
lats (hapsburg.PackagesSupport.simData.Simulator attribute)
limit_range_for_scale() (hapsburg.PackagesSupport.sqrt_scale.SquareRootScale method)
ll_individual() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
load_bad_areas() (in module hapsburg.figures.plot_individual_roh)
load_data() (hapsburg.hmm_inference.HMM_Analyze method)
(hapsburg.postprocessing.PostProcessing method)
(hapsburg.preprocessing.PreProcessing method)
(hapsburg.preprocessing.PreProcessingEigenstrat method)
(hapsburg.preprocessing.PreProcessingFolder method)
(hapsburg.preprocessing.PreProcessingHDF5 method)
(hapsburg.preprocessing.PreProcessingHDF5_lowmem method)
(in module hapsburg.figures.plot_posterior)
load_eigenstrat() (in module hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat)
load_emission_model() (hapsburg.hmm_inference.HMM_Analyze method)
(in module hapsburg.emissions)
load_h5() (hapsburg.preprocessing.PreProcessingHDF5 method)
(in module hapsburg.PackagesSupport.h5_python.h5_functions)
load_ind_df() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
load_individual_roh() (in module hapsburg.figures.plot_individual_roh)
load_linkage_map() (hapsburg.preprocessing.PreProcessingFolder method)
load_objects() (hapsburg.hmm_inference.HMM_Analyze method)
load_Postprocessing() (in module hapsburg.postprocessing)
load_postprocessing_model() (hapsburg.hmm_inference.HMM_Analyze method)
load_preprocessing() (in module hapsburg.preprocessing)
load_preprocessing_model() (hapsburg.hmm_inference.HMM_Analyze method)
load_roh() (in module hapsburg.figures.plot_individual_roh)
load_roh_vec() (in module hapsburg.PackagesSupport.fit_ne)
load_secondary_objects() (hapsburg.hmm_inference.HMM_Analyze method)
load_snp_df() (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad method)
load_transition_model() (hapsburg.hmm_inference.HMM_Analyze method)
(in module hapsburg.transitions)
logit() (hapsburg.PackagesSupport.simData.MultiVariateNormalLD method)
loglikeobs() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
lowess (in module hapsburg.figures.plot_timelines)
lowess_sqrt() (in module hapsburg.figures.plot_timelines)
M
main() (in module hapsburg.hapCon_ROH)
(in module hapsburg.hapCONX)
markers_called() (hapsburg.preprocessing.PreProcessingHDF5 method)
max_gap (hapsburg.postprocessing.PostProcessing attribute)
max_mm_rate (hapsburg.preprocessing.PreProcessingHDF5 attribute)
merge (hapsburg.postprocessing.PostProcessing attribute)
merge_2hdf() (hapsburg.preprocessing.PreProcessingHDF5 method)
merge_called_blocks() (hapsburg.postprocessing.PostProcessing method)
(in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
merge_called_blocks_custom() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
merge_es_hdf5() (hapsburg.preprocessing.PreProcessingEigenstrat method)
merge_in_ld_map() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
meta_path_ref (hapsburg.preprocessing.PreProcessingHDF5 attribute)
mid_bins (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
min_len1 (hapsburg.postprocessing.PostProcessing attribute)
min_len2 (hapsburg.postprocessing.PostProcessing attribute)
MLE_ROH_Ne (class in hapsburg.PackagesSupport.fit_ne)
mmr_call() (hapsburg.hmm_inference.HMM_Analyze method)
MMR_PostProcessing (class in hapsburg.postprocessing)
Model_Emissions (class in hapsburg.emissions)
Model_Transitions (class in hapsburg.transitions)
modify_posterior0() (hapsburg.postprocessing.MMR_PostProcessing method)
(hapsburg.postprocessing.PostProcessing method)
module
hapsburg
hapsburg.emissions
hapsburg.figures
hapsburg.figures.plot_bars
hapsburg.figures.plot_ibdx
hapsburg.figures.plot_individual_roh
hapsburg.figures.plot_posterior
hapsburg.figures.plot_timelines
hapsburg.func
hapsburg.hapCon_ROH
hapsburg.hapCONX
hapsburg.hmm_inference
hapsburg.PackagesSupport
hapsburg.PackagesSupport.fit_ne
hapsburg.PackagesSupport.h5_python
hapsburg.PackagesSupport.h5_python.h5_functions
hapsburg.PackagesSupport.hapsburg_run
hapsburg.PackagesSupport.loadEigenstrat
hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat
hapsburg.PackagesSupport.loadEigenstrat.saveHDF5
hapsburg.PackagesSupport.parallel_runs
hapsburg.PackagesSupport.parallel_runs.helper_functions
hapsburg.PackagesSupport.pp_individual_roh_csvs
hapsburg.PackagesSupport.roh_expectations
hapsburg.PackagesSupport.simData
hapsburg.PackagesSupport.sqrt_scale
hapsburg.postprocessing
hapsburg.preprocessing
hapsburg.transitions
move_X_to_parent_folder() (in module hapsburg.PackagesSupport.parallel_runs.helper_functions)
mpileup2hdf5() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
(in module hapsburg.PackagesSupport.loadEigenstrat.saveHDF5)
mpileup2hdf5_damageAware() (in module hapsburg.PackagesSupport.loadEigenstrat.saveHDF5)
mpileups2hdf5() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
multi_run() (in module hapsburg.PackagesSupport.parallel_runs.helper_functions)
MultiVariateNormalLD (class in hapsburg.PackagesSupport.simData)
N
n_ref (hapsburg.hmm_inference.HMM_Analyze attribute)
(hapsburg.preprocessing.PreProcessing attribute)
(hapsburg.transitions.Transitions attribute)
name (hapsburg.PackagesSupport.sqrt_scale.SquareRootScale attribute)
new_column() (in module hapsburg.figures.plot_ibdx)
nind (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad attribute)
nsnp (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad attribute)
O
ob_stat (hapsburg.hmm_inference.HMM_Analyze attribute)
(hapsburg.PackagesSupport.simData.Simulator attribute)
(in module hapsburg.emissions)
only_calls (hapsburg.preprocessing.PreProcessingHDF5 attribute)
optimize_ll_contamANDerr() (hapsburg.hmm_inference.HMM_Analyze method)
optimize_ll_contamination() (hapsburg.hmm_inference.HMM_Analyze method)
optimize_ll_contamination_BFGS() (hapsburg.hmm_inference.HMM_Analyze method)
optimze_ll_transition_param() (hapsburg.hmm_inference.HMM_Analyze method)
optional_postprocessing() (hapsburg.preprocessing.PreProcessingEigenstrat method)
(hapsburg.preprocessing.PreProcessingHDF5 method)
(hapsburg.preprocessing.PreProcessingHDF5_lowmem method)
out_folder (hapsburg.preprocessing.PreProcessingHDF5Sim attribute)
output (hapsburg.hmm_inference.HMM_Analyze attribute)
(hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
(hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad attribute)
(hapsburg.postprocessing.PostProcessing attribute)
(hapsburg.preprocessing.PreProcessing attribute)
(hapsburg.preprocessing.PreProcessingFolder attribute)
output_dims (hapsburg.PackagesSupport.sqrt_scale.SquareRootScale.InvertedSquareRootTransform attribute)
(hapsburg.PackagesSupport.sqrt_scale.SquareRootScale.SquareRootTransform attribute)
overhang (hapsburg.hmm_inference.HMM_Analyze attribute)
P
p (hapsburg.emissions.Diploid_GT_Emissions attribute)
(hapsburg.emissions.Model_Emissions attribute)
(hapsburg.emissions.RC_Model_Emissions attribute)
(hapsburg.PackagesSupport.simData.BinomSimRefNoLD attribute)
p_model (hapsburg.hmm_inference.HMM_Analyze attribute)
packed (hapsburg.preprocessing.PreProcessingEigenstrat attribute)
(hapsburg.preprocessing.PreProcessingEigenstratX attribute)
path_targets (hapsburg.preprocessing.PreProcessingEigenstrat attribute)
(hapsburg.preprocessing.PreProcessingEigenstratX attribute)
(hapsburg.preprocessing.PreProcessingHDF5 attribute)
(hapsburg.preprocessing.PreProcessingHDF5Sim attribute)
pCon (hapsburg.emissions.RC_Model_Emissions_withContamination attribute)
(hapsburg.hmm_inference.HMM_Analyze attribute)
plot_bar_ax() (in module hapsburg.figures.plot_bars)
plot_chromosome() (in module hapsburg.figures.plot_individual_roh)
plot_close_kin() (in module hapsburg.figures.plot_bars)
plot_colorbar_age() (in module hapsburg.figures.plot_timelines)
plot_ibd_curves() (in module hapsburg.figures.plot_ibdx)
plot_IBD_fracs() (in module hapsburg.figures.plot_ibdx)
plot_ld_r2() (hapsburg.PackagesSupport.simData.SimRef method)
plot_legend_only() (in module hapsburg.figures.plot_bars)
plot_lowess_smoothing() (in module hapsburg.figures.plot_timelines)
plot_map_ax() (in module hapsburg.figures.plot_timelines)
plot_map_time() (in module hapsburg.figures.plot_timelines)
plot_ne_dct() (in module hapsburg.figures.plot_ibdx)
plot_panel_row() (in module hapsburg.figures.plot_bars)
plot_pde_individual() (in module hapsburg.figures.plot_individual_roh)
plot_posterior() (in module hapsburg.figures.plot_posterior)
plot_posterior_cm() (in module hapsburg.figures.plot_posterior)
plot_roh_individual() (in module hapsburg.figures.plot_individual_roh)
plot_scatter_by_color() (in module hapsburg.figures.plot_timelines)
plot_violin_ax() (in module hapsburg.figures.plot_timelines)
plot_viterbi() (in module hapsburg.figures.plot_posterior)
pos (hapsburg.hmm_inference.HMM_Analyze attribute)
post (hapsburg.postprocessing.PostProcessing attribute)
post_model (hapsburg.hmm_inference.HMM_Analyze attribute)
post_process_roh_df() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
post_process_roh_df1() (in module hapsburg.figures.plot_individual_roh)
post_processing() (hapsburg.hmm_inference.HMM_Analyze method)
posterior (hapsburg.hmm_inference.HMM_Analyze attribute)
postprocess_iid() (in module hapsburg.PackagesSupport.parallel_runs.helper_functions)
PostProcessing (class in hapsburg.postprocessing)
PostProcessingX (class in hapsburg.postprocessing)
pp (in module hapsburg.preprocessing)
pp_individual_roh() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
pp_X_roh() (in module hapsburg.PackagesSupport.pp_individual_roh_csvs)
pre_compute_transition_matrix() (hapsburg.hmm_inference.HMM_Analyze method)
prefix_out_data (hapsburg.preprocessing.PreProcessingHDF5 attribute)
(hapsburg.preprocessing.PreProcessingHDF5Sim attribute)
preload() (in module hapsburg.PackagesSupport.hapsburg_run)
prep_3x3matrix() (in module hapsburg.hmm_inference)
prep_dfs_plot_exact() (in module hapsburg.figures.plot_bars)
prep_label() (in module hapsburg.figures.plot_timelines)
prep_xlabels() (in module hapsburg.figures.plot_bars)
prepare_dfs_plot() (in module hapsburg.figures.plot_bars)
prepare_path() (in module hapsburg.PackagesSupport.parallel_runs.helper_functions)
prepare_path_general() (in module hapsburg.PackagesSupport.hapsburg_run)
prepare_rmap() (hapsburg.hmm_inference.HMM_Analyze method)
PreProcessing (class in hapsburg.preprocessing)
PreProcessingEigenstrat (class in hapsburg.preprocessing)
PreProcessingEigenstratX (class in hapsburg.preprocessing)
PreProcessingFolder (class in hapsburg.preprocessing)
PreProcessingHDF5 (class in hapsburg.preprocessing)
PreProcessingHDF5_lowmem (class in hapsburg.preprocessing)
PreProcessingHDF5Sim (class in hapsburg.preprocessing)
print_block_nr() (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
print_memory_usage() (in module hapsburg.hmm_inference)
process_read_counts() (in module hapsburg.figures.plot_posterior)
pull_down_pileup() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
pure_stat (hapsburg.PackagesSupport.simData.Simulator attribute)
R
r_map (hapsburg.hmm_inference.HMM_Analyze attribute)
(hapsburg.transitions.Transitions attribute)
random_allele (hapsburg.preprocessing.PreProcessingHDF5 attribute)
RC_Model_Emissions (class in hapsburg.emissions)
RC_Model_Emissions_withContamination (class in hapsburg.emissions)
readcounts (hapsburg.preprocessing.PreProcessingFolder attribute)
(hapsburg.preprocessing.PreProcessingHDF5 attribute)
ref_haps (hapsburg.emissions.Diploid_GT_Emissions attribute)
(hapsburg.emissions.Model_Emissions attribute)
(hapsburg.emissions.RC_Model_Emissions attribute)
ref_sim (hapsburg.PackagesSupport.simData.Simulator attribute)
ref_states (hapsburg.hmm_inference.HMM_Analyze attribute)
(hapsburg.PackagesSupport.simData.Simulator attribute)
refs (hapsburg.PackagesSupport.simData.SimRef attribute)
rlen (hapsburg.PackagesSupport.loadEigenstrat.loadEigenstrat.EigenstratLoad attribute)
roh_df (hapsburg.postprocessing.PostProcessing attribute)
roh_in (hapsburg.PackagesSupport.simData.BinomSim attribute)
(hapsburg.PackagesSupport.simData.BinomSimCopyBoth attribute)
(hapsburg.transitions.Model_Transitions attribute)
roh_jump (hapsburg.PackagesSupport.simData.BinomSim attribute)
(hapsburg.PackagesSupport.simData.BinomSimCopyBoth attribute)
(hapsburg.transitions.Model_Transitions attribute)
roh_min_l_final (hapsburg.postprocessing.PostProcessing attribute)
roh_min_l_initial (hapsburg.postprocessing.PostProcessing attribute)
roh_out (hapsburg.PackagesSupport.simData.BinomSim attribute)
(hapsburg.PackagesSupport.simData.BinomSimCopyBoth attribute)
(hapsburg.transitions.Model_Transitions attribute)
roh_pdf_allchr_N() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
roh_pdf_allchr_rel() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
roh_pdf_allchr_t_N() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
roh_pdf_N() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
roh_pdf_rel() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
roh_pdf_t_N() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
S
samples_field (hapsburg.preprocessing.PreProcessingHDF5 attribute)
sanity_checks (hapsburg.hmm_inference.HMM_Analyze attribute)
save (hapsburg.hmm_inference.HMM_Analyze attribute)
(hapsburg.postprocessing.PostProcessing attribute)
(hapsburg.preprocessing.PreProcessing attribute)
(hapsburg.preprocessing.PreProcessingFolder attribute)
save_data() (hapsburg.PackagesSupport.simData.Simulator method)
save_data_h5() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
save_fp (hapsburg.hmm_inference.HMM_Analyze attribute)
save_hdf5() (in module hapsburg.PackagesSupport.loadEigenstrat.saveHDF5)
save_info() (hapsburg.preprocessing.PreProcessingHDF5 method)
save_parameters() (hapsburg.PackagesSupport.simData.BinomSim method)
(hapsburg.PackagesSupport.simData.Simulator method)
segM (hapsburg.preprocessing.PreProcessing attribute)
sep (hapsburg.preprocessing.PreProcessingEigenstrat attribute)
(hapsburg.preprocessing.PreProcessingEigenstratX attribute)
set_cons_spacing() (hapsburg.PackagesSupport.simData.BinomSim method)
(hapsburg.PackagesSupport.simData.BinomSimCopyBoth method)
set_default_locators_and_formatters() (hapsburg.PackagesSupport.sqrt_scale.SquareRootScale method)
set_output_folder() (hapsburg.preprocessing.PreProcessing method)
(hapsburg.preprocessing.PreProcessingEigenstratX method)
set_params() (hapsburg.emissions.Emissions method)
(hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne method)
(hapsburg.PackagesSupport.simData.BinomSim method)
(hapsburg.PackagesSupport.simData.BinomSimCopyBoth method)
(hapsburg.PackagesSupport.simData.SimRef method)
(hapsburg.postprocessing.PostProcessing method)
(hapsburg.preprocessing.PreProcessing method)
(hapsburg.transitions.Transitions method)
set_ref_sim() (hapsburg.PackagesSupport.simData.Simulator method)
sim (in module hapsburg.PackagesSupport.simData)
sim_copying() (hapsburg.PackagesSupport.simData.BinomSim method)
sim_copying_inroh() (hapsburg.PackagesSupport.simData.BinomSimCopyBoth method)
sim_roh_inout() (hapsburg.PackagesSupport.simData.BinomSimCopyBoth method)
SimRef (class in hapsburg.PackagesSupport.simData)
simulate_full() (hapsburg.PackagesSupport.simData.Simulator method)
simulate_latent() (hapsburg.PackagesSupport.simData.BinomSim method)
(hapsburg.PackagesSupport.simData.BinomSimCopyBoth method)
(hapsburg.PackagesSupport.simData.Simulator method)
simulate_ref() (hapsburg.PackagesSupport.simData.Simulator method)
simulate_refs() (hapsburg.PackagesSupport.simData.BinomSimRefNoLD method)
(hapsburg.PackagesSupport.simData.MultiVariateNormalLD method)
(hapsburg.PackagesSupport.simData.SimRef method)
Simulator (class in hapsburg.PackagesSupport.simData)
sloppyROH_cumsum() (in module hapsburg.func)
snp_extend() (hapsburg.postprocessing.PostProcessing method)
snps_extend (hapsburg.postprocessing.PostProcessing attribute)
spacing (hapsburg.PackagesSupport.simData.BinomSim attribute)
(hapsburg.PackagesSupport.simData.BinomSimCopyBoth attribute)
split_up_inferred_roh() (in module hapsburg.PackagesSupport.parallel_runs.helper_functions)
split_up_roh_df() (in module hapsburg.PackagesSupport.parallel_runs.helper_functions)
SquareRootScale (class in hapsburg.PackagesSupport.sqrt_scale)
SquareRootScale.InvertedSquareRootTransform (class in hapsburg.PackagesSupport.sqrt_scale)
SquareRootScale.SquareRootTransform (class in hapsburg.PackagesSupport.sqrt_scale)
start (hapsburg.hmm_inference.HMM_Analyze attribute)
start_params (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
std_Ne_roh() (in module hapsburg.figures.plot_bars)
summary (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
T
t_model (hapsburg.hmm_inference.HMM_Analyze attribute)
theoretical_shr (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
to_read_counts() (hapsburg.preprocessing.PreProcessingEigenstrat method)
to_vcf() (in module hapsburg.PackagesSupport.h5_python.h5_functions)
trans_mat (hapsburg.PackagesSupport.fit_ne.MLE_ROH_Ne attribute)
(hapsburg.transitions.Transitions attribute)
transform() (hapsburg.PackagesSupport.sqrt_scale.SquareRootScale.InvertedSquareRootTransform method)
transform_non_affine() (hapsburg.PackagesSupport.sqrt_scale.SquareRootScale.SquareRootTransform method)
Transitions (class in hapsburg.transitions)
V
v_path (hapsburg.hmm_inference.HMM_Analyze attribute)
var_roh_len_in_bin_N() (hapsburg.PackagesSupport.roh_expectations.Expected_Roh method)
viterbi_path_p() (in module hapsburg.func)
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