Man pages for jtmccr1/HIVEr
Analysis of transmission and intrahost iSNV data taken as part of the HIVE cohort

accuracy_stringentSequencing specificity and sensitivity
betabin_simSimulate transmission Beta binomial model
betabin_sim_helperbeta bin sim helper
com_sample_transRandomly sample a transmission tibble based on a list of...
correct_idCorrect numerical Ids In our analysis the Id column refers to...
dist_probFit a distribution to pair_wise bottlenecks
dist_prob_wrapperMake distribution specific functions to fit distribution
dist_tpGet the genetic distance between two samples .
diverse_sitesGet sites with diverisity
dzpoisPMF of a zero truncated Poisson distribution
equal_compareFair base call comparisons.
finding_validValidating transmission pairs
get_closeFinding SPECID for transmission pairs
get_doubleGet all ENROLLID that have two SPECID in a season with same...
get_freqsGet and compare the frequencies of mutations in two samples.
getting_tpFinding transmission pairs
g_ftLikelihood of frequency starting at 0
is_wholenumberIs this a whole number
L.Nb.betaBetabinomial Likelihood functions
longform_pairsConvert short paired data to long paired data.
math_fitThe probability of lambda for a loci
model_summarySummarize model likelihoods
monomorphicSet monomorphic sites to freq =1
mut_model_LLMutation rate and Ne from spectrum
not_detectedProbability of not detecting a polymorphism This is the...
only_onePicking one sample per person
p0Mutational model- non polmorphic
p_allProbability of drawing an allele n times in n draws
pa_simSimulate transmission Presence absence model
pa_sim_helperPA sim helper
polish_freqPolishing compared frequencies.
qualityIdentify quality variants
read_rbindRead in a list of files
rzpoisRandomly sample a zero truncated Poisson
sample_transRandomly sample a transmission data.frame without any...
short_pairsConvert long paired data to short paired data.
sift_dupsSift duplicate calls Take in a data frame of one mutation...
simulationsSimulate probability of transmission based on frequency
small_community.compiSNV comparison between samples
small_isnviSNV present in samples
small_metaA small meta data file
small_transTransmission pairs iSNV
split_pathSplit a file path at /
trans_fitFit the transmission model
variantsVariant data
jtmccr1/HIVEr documentation built on Aug. 5, 2018, 2:04 a.m.