Man pages for jtmccr1/HIVEr
Analysis of transmission and intrahost iSNV data taken as part of the HIVE cohort
| accuracy_stringent | Sequencing specificity and sensitivity |
| betabin_sim | Simulate transmission Beta binomial model |
| betabin_sim_helper | beta bin sim helper |
| com_sample_trans | Randomly sample a transmission tibble based on a list of... |
| correct_id | Correct numerical Ids In our analysis the Id column refers to... |
| dist_prob | Fit a distribution to pair_wise bottlenecks |
| dist_prob_wrapper | Make distribution specific functions to fit distribution |
| dist_tp | Get the genetic distance between two samples . |
| diverse_sites | Get sites with diverisity |
| dzpois | PMF of a zero truncated Poisson distribution |
| equal_compare | Fair base call comparisons. |
| finding_valid | Validating transmission pairs |
| get_close | Finding SPECID for transmission pairs |
| get_double | Get all ENROLLID that have two SPECID in a season with same... |
| get_freqs | Get and compare the frequencies of mutations in two samples. |
| getting_tp | Finding transmission pairs |
| g_ft | Likelihood of frequency starting at 0 |
| is_wholenumber | Is this a whole number |
| L.Nb.beta | Betabinomial Likelihood functions |
| longform_pairs | Convert short paired data to long paired data. |
| math_fit | The probability of lambda for a loci |
| model_summary | Summarize model likelihoods |
| monomorphic | Set monomorphic sites to freq =1 |
| mut_model_LL | Mutation rate and Ne from spectrum |
| not_detected | Probability of not detecting a polymorphism This is the... |
| only_one | Picking one sample per person |
| p0 | Mutational model- non polmorphic |
| p_all | Probability of drawing an allele n times in n draws |
| pa_sim | Simulate transmission Presence absence model |
| pa_sim_helper | PA sim helper |
| polish_freq | Polishing compared frequencies. |
| quality | Identify quality variants |
| read_rbind | Read in a list of files |
| rzpois | Randomly sample a zero truncated Poisson |
| sample_trans | Randomly sample a transmission data.frame without any... |
| short_pairs | Convert long paired data to short paired data. |
| sift_dups | Sift duplicate calls Take in a data frame of one mutation... |
| simulations | Simulate probability of transmission based on frequency |
| small_community.comp | iSNV comparison between samples |
| small_isnv | iSNV present in samples |
| small_meta | A small meta data file |
| small_trans | Transmission pairs iSNV |
| split_path | Split a file path at / |
| trans_fit | Fit the transmission model |
| variants | Variant data |
