Man pages for mccoy-lab/rhapsodi
R haploid sperm/oocyte data imputation
| betaregmodel_20220718 | Trained beta regression model for automatic phasing window... |
| build_hmm | Build a model to assign haplotypes to each gamete |
| calculate_window_size | A function to automatically calculate a preferred window size... |
| cbind_pos | This function adds an index and a pos column to dataframes |
| dataACGT | Simulated Sperm-seq data A/C/G/T/NA encoded |
| discover_meiotic_recombination | A function to drive and report meiotic recombination... |
| export_data | A function to export the data from rhapsodi |
| fill_na | A function to fill in missing data from each gamete |
| find_recomb_spots | A function to find recombination breakpoint regions for a... |
| get_mode | A function to find the more common allele or NA at each SNP |
| impute_gamete_genotypes | A function to drive the assignment and reporting of the... |
| invert_bits | A function to invert the values in a data frame or matrix |
| phase_donor_haplotypes | A function to drive the phasing and reporting of the two... |
| read_data | A function to read in the sparse gamete sequencing data... |
| recode_gametes | A function to assign each allele to a haplotype or an NA if... |
| reconstruct_hap | A function to reconstruct the donor haplotypes using data... |
| record_ref_alt | This function can be used to append the reference and... |
| re_recode_gametes | A function to turn a matrix of gamete haplotypes by position... |
| rhapsodi_autorun | This function can be used to run all steps of rhapsodi |
| run_hmm | A function that assigns the position in each gamete to the... |
| sim01NA42 | Simulated Sperm-seq data 0/1/NA encoded |
| sim_add_de_novo_mut | This function adds de novo mutations (DNM) to the generated... |
| sim_add_na_flatten | This function changes random indices to NA, in effect... |
| sim_add_seq_error | This function inverts a bit at random indices in effect... |
| sim_add_to_na_flatten | This function overwrites NAs from random indices with "real"... |
| sim_assess_gam_imputation | This function assesses the effectiveness of rhapsodi's gamete... |
| sim_assess_it | This function drives the assessment of all 3 parts of... |
| sim_assess_phasing | This function assesses the effectiveness of rhapsodi's... |
| sim_assess_recomb | This function assesses the effectiveness of rhapsodi's... |
| sim_autorun | This is the simulation autorun that generates data, calls... |
| sim_completeness | This function computes the completeness of a haplotype |
| sim_filter_generated_data | This function filters the generated gamete data so that the... |
| sim_find_cov_from_mgr | This function computes the coverage given the desired missing... |
| sim_find_fn | This function finds the number of false negatives when... |
| sim_find_fp | This function finds the number of false positives when... |
| sim_find_mgr_from_cov | This function computes the missing genotype rate given the... |
| sim_find_num_crossovers | This function finds the number of crossovers for each gamete |
| sim_find_num_nas | This function computes the number of NAs that should be used... |
| sim_find_tn | This function finds the number of true negatives when... |
| sim_find_tp | This function finds the number of true positives when... |
| sim_gamete_killing | This function is used to run the generative model to simulate... |
| sim_gene_conversion | This function is used to run the generative model to simulate... |
| sim_generate_donor_hap | This function generates the diploid donor haplotypes of... |
| sim_generate_gam | This function is used to generate the fully known gamete... |
| sim_generate_global | This function simulates fully known gamete genotypes given a... |
| sim_hamming_distance_ignoreNA | This function computes the hamming distance (or the opposite... |
| sim_lhs | This function computes the largest haplotype segment |
| sim_metrics | This function computes and returns metrics given the number... |
| sim_run_generative_model | This function runs the generative model to simulate input... |
| sim_run_generative_model_with_TD | This function runs the generative model to simulate input... |
| sim_ser | This function computes the switch error rate |
| split_with_overlap | A function to separate the gamete SNP positions into... |
| stitch_haplotypes | A function to stitch overlapping windows together into the... |
| unsmooth | A function to unsmooth or replace original reads for the... |
