Man pages for SLeviyang/RegressHaplo
Haplotype Reconstruction Using Penalized Regression

adjacency_matrix.read_tableCreate edge matrix for read graph
AL.engineCompute the augmented lagrangian
all_pos.read_tableReturn the positions covered by each read group in a read...
BAM_file_position_pair_frequencies.errorExtract the position pair frequencies from read table...
BAM_pileupCalculate pileup for each position of reference from BAM file
bam_to_variant_calls.pipelineGiven a bam file, create variant call file
best_K.RegressHaploSolutionsDetermines the best fit solution
calculate_position_pair_error.errorCalculate error for each position pair
clean.read_tableClean read table
compare.HaploCompare frequencies and haplotypes of H1 using the...
compute_solution.RegressHaploFit regression for a given rho
consensusReturns a consensus sequence given a VSeqTools_pileup object
consensus.read_tableReturn the consensus sequence at each position of the read...
consistent_haplotypes_across_loci.read_tableSplit read table into loci with no spanning reads, create...
consistent_haplotypes.read_tableSplit read table into loci with no spanning single end reads,...
coverage.read_tableReturn coverage at each position in read table
create_position_pair_comparison_read_table.errorCreate a read table for analyzing frequencies of positions...
create_refspace_seqConverts reads to a sequence in the reference space
divergence_variant_callsCalls nt positions at which a BAM file differs from a base...
end_pos.read_tableReturn the end position of each read group in a read table
error_filter.read_tableRemove reads that are below error noise.
filter_and_optimize.RegressHaploGenerate consistent haplotypes for a read table and, if...
filter_true_variants.read_tableFilter read table for variant calls
fix_out_dirAdd a / to out_dir if it is not there
full_pipelineExecute full RegressHaplo pipeline
get_error_rateEstimate error rate of pileup
get_position_pair_comparison_read_table.errorGet 'position_pair_read_table.csv' from directory
get_solutions_haplotype_reconstruction.pipelineHaplotype reconstruction of given solution
get_solutions_summary.pipelineSummary of regression fits over all starting points
get_variant_call_posGet variant call positions from a VSeqTools_variant_call...
grad_AL.engineCompute gradient of augmented lagrangian
HaploHaplo object construct
haplotype_match.readFitDetermine haplotypes that match a nucleotide pattern
haplotypes_to_fasta.pipelineGiven RegressHaplo haplotypes file, produce fasta file...
haplotypes_to_parameters.pipelineGiven a read table and loci, create parameter files for...
helloHello, World!
loci_to_haplotypes.pipelineGiven loci, create global haplotypes
max_Hessian_eigenvalue.engineCompute maximum eigenvalue of Hessian to scale gradient
merge_haplotypes.read_tableA helper function that create haplotype permutations from a...
nofilter_and_optimize.RegressHaploGenerate consistent haplotypes for a read table and applies a...
nucs_at_pos.read_tableReturn nucleotide counts at each position
paired_end_read_tableA helper function that creates read tables from paired end...
parameters.RegressHaploGenerate the y vector and P matrix of the RegressHaplo...
parameters_to_solutions.pipelineGiven a parameter files, run RegressHaplo to produce multiple...
parse_solutions.RegressHaploSolutionsParse solutions matrix
paths_exceed_limit.read_tableQuickly determine the number of paths in an adjacency matrix...
paths_to_haplotypes.read_tableA helper function that converts read graph paths to haplotype...
penalized_regression_parameters.RegressHaploReturns the matrices and vectors associated with the...
penalized_regression.RegressHaploSolves min_pi |y - P*pi|^2 + rho*pi^T*M*pi
plot_pair_position_error.errorPlot the position errors
plot.readFitVisualize a readfit object
plot_single_position.errorPlot the position errors
position_fit.readFitReturn a readFit object base on nucleotide positions
position_pairs.errorGet position pairs with threshold coverage
pos_names.read_tableReturns positions of read table as character vector
readFitreadFit constructor
read_fit.readFitBuild a readFit object base on reads
reads_covering_haplotypes.read_tableFor each haplotype, return reads that match haplotype at...
reads_covering_positions.read_tableFor each position, return reads that cover the position
read_tableRead table constructor
read_table_to_loci.pipelineGiven a read table, split variable positions into loci
reconstructed_position_pair_frequencies.errorExtract the position pair frequencies from haplotypes
RegressHaploSolutionsLoads a set of solutions created by solutions.RegressHaplo
regroup.read_tableMerges identical read over an edited read table
seq.read_tableReturn the nucleotides in each read group of a read table
set_pos_names.HaploSet the position names for the characters (nucleotides)...
single_end_read_tableA helper function that creates read tables from single end...
single_position.errorDetermine the frequency error at variable positions
solutions.RegressHaploSolve the RegressHaplo optimization repeatedly
solutions_to_haplotypes.pipelineGiven a RegressHaplo solutions file, determine optimal...
split_allele.readFitSplit alleles while accounting for insertions
split_paired_ends.read_tableSplit reads which have a gap between the paired ends
split.read_tableSplit a read table into two read tables.
split_unlinked_loci.read_tableSplit a read_table into multiple read_tables representing...
start_pos.read_tableReturn the start position of each read group in a read table
subset.read_tableLimit read table to a subset of positions
template_alleles.read_tableReturn all alleles matching a read template
template_fit.readFitBuild a readFit object base on templates. This is a generic...
template_indices.read_tableReturn read indices corresponding to the template
templates.read_tableRetrieve all templates matching at least one read in the read...
unique.HaploReturns Haplo object with identical haplotype frequencies...
unlinked_pos.read_tableDetermines loci in read table that have no overlapping reads
variant_callsReturns variant calls given a VSeqTools_pileup object
variant_calls_cutoffReturns variant calls given a VSeqTools_pileup object
variant_calls_sigReturns variant calls given a VSeqTools_pileup object
variant_calls_to_read_table.pipelineGiven variant calls and a bam file, create a read table
SLeviyang/RegressHaplo documentation built on Aug. 26, 2017, 10:22 p.m.