Files in SLeviyang/RegressHaplo
Haplotype Reconstruction Using Penalized Regression

DESCRIPTION
MATLAB/chkstop.m
MATLAB/control.m
MATLAB/estL.m
MATLAB/fgf.m
MATLAB/quickfind.m
MATLAB/sl.m
NAMESPACE
R/Haplo.R R/RegressHaplo_analyze_solutions.R R/RegressHaplo_create_solutions.R R/RegressHaplo_engine.R R/RegressHaplo_util.R R/RegressHaplo_workflow.R R/RegressHoplo_engine_fast.R R/VSeqTools_pileup.R R/error.R R/readFit.R R/read_table.R README.md
example/data/.DS_Store
example/data/example.bam
example/data/example.bam.bai
example/example_readme.Rmd example/example_readme.pdf
example/output/P.csv
example/output/final_haplo.csv
example/output/final_haplo.fasta
example/output/h.csv
example/output/loci.csv
example/output/raw_read_table.csv
example/output/read_table.csv
example/output/solutions.csv
example/output/variant_calls.csv
example/output/y.csv
man/AL.engine.Rd man/BAM_file_position_pair_frequencies.error.Rd man/BAM_pileup.Rd man/Haplo.Rd man/RegressHaploSolutions.Rd man/adjacency_matrix.read_table.Rd man/all_pos.read_table.Rd man/bam_to_variant_calls.pipeline.Rd man/best_K.RegressHaploSolutions.Rd man/calculate_position_pair_error.error.Rd man/clean.read_table.Rd man/compare.Haplo.Rd man/compute_solution.RegressHaplo.Rd man/consensus.Rd man/consensus.read_table.Rd man/consistent_haplotypes.read_table.Rd man/consistent_haplotypes_across_loci.read_table.Rd man/coverage.read_table.Rd man/create_position_pair_comparison_read_table.error.Rd man/create_refspace_seq.Rd man/divergence_variant_calls.Rd man/end_pos.read_table.Rd man/error_filter.read_table.Rd man/filter_and_optimize.RegressHaplo.Rd man/filter_true_variants.read_table.Rd man/fix_out_dir.Rd man/full_pipeline.Rd man/get_error_rate.Rd man/get_position_pair_comparison_read_table.error.Rd man/get_solutions_haplotype_reconstruction.pipeline.Rd man/get_solutions_summary.pipeline.Rd man/get_variant_call_pos.Rd man/grad_AL.engine.Rd man/haplotype_match.readFit.Rd man/haplotypes_to_fasta.pipeline.Rd man/haplotypes_to_parameters.pipeline.Rd man/hello.Rd man/loci_to_haplotypes.pipeline.Rd man/max_Hessian_eigenvalue.engine.Rd man/merge_haplotypes.read_table.Rd man/nofilter_and_optimize.RegressHaplo.Rd man/nucs_at_pos.read_table.Rd man/paired_end_read_table.Rd man/parameters.RegressHaplo.Rd man/parameters_to_solutions.pipeline.Rd man/parse_solutions.RegressHaploSolutions.Rd man/paths_exceed_limit.read_table.Rd man/paths_to_haplotypes.read_table.Rd man/penalized_regression.RegressHaplo.Rd man/penalized_regression_parameters.RegressHaplo.Rd man/plot.readFit.Rd man/plot_pair_position_error.error.Rd man/plot_single_position.error.Rd man/pos_names.read_table.Rd man/position_fit.readFit.Rd man/position_pairs.error.Rd man/readFit.Rd man/read_fit.readFit.Rd man/read_table.Rd man/read_table_to_loci.pipeline.Rd man/reads_covering_haplotypes.read_table.Rd man/reads_covering_positions.read_table.Rd man/reconstructed_position_pair_frequencies.error.Rd man/regroup.read_table.Rd man/seq.read_table.Rd man/set_pos_names.Haplo.Rd man/single_end_read_table.Rd man/single_position.error.Rd man/solutions.RegressHaplo.Rd man/solutions_to_haplotypes.pipeline.Rd man/split.read_table.Rd man/split_allele.readFit.Rd man/split_paired_ends.read_table.Rd man/split_unlinked_loci.read_table.Rd man/start_pos.read_table.Rd man/subset.read_table.Rd man/template_alleles.read_table.Rd man/template_fit.readFit.Rd man/template_indices.read_table.Rd man/templates.read_table.Rd man/unique.Haplo.Rd man/unlinked_pos.read_table.Rd man/variant_calls.Rd man/variant_calls_cutoff.Rd man/variant_calls_sig.Rd man/variant_calls_to_read_table.pipeline.Rd
SLeviyang/RegressHaplo documentation built on Aug. 26, 2017, 10:22 p.m.