Usage
fullRepertoire(max.seq.num, max.timer, SHM.method, baseline.mut, SHM.branch.prob, SHM.branch.param, SHM.nuc.prob, species, VDJ.branch.prob, proportion.sampled, sample.time, max.tree.num)
Arguments
max.seq.num
The maximum number of tips allowed at the end of the simulation. The simulation
will end when either this or the max.timer is reached. Note - this function does not take clonal
frequency into account. This parameter resembles the species richness, or the measure of unique sequences
in the repertoire.
max.timer
The maximum number of time steps allowed during the simulation. The simulation
will end when either this or the max.seq.num is reached.
SHM.method
The mode of SHM speciation events. Options are either: "poisson","data","motif","wrc", and "all". Specifying
"poisson" will result in mutations that can occur anywhere in the heavy chain region, with each nucleotide having an equal probability
for a mutation event. Specifying "data" focuses mutation events during SHM in the CDR regions (based on IMGT), and
there will be an increased probability for transitions (and decreased probability for transversions). Specifying
"motif" will cause neighbor dependent mutations based on a mutational matrix from high throughput sequencing
data sets (Yaari et al., Frontiers in Immunology, 2013). "wrc" allows for only the WRC mutational hotspots
to be included (where W equals A or T and R equals A or G). Specifying "all" will use all four types of mutations
during SHM branching events, where the weights for each can be specified in the "SHM.nuc.prob" parameter.
baseline.mut
Specifies the probability (gamma) for each nucleotide to be mutated inbetween speciation events. These
mutations do not cause any branching events. This parameter gives each site a probability to be mutated
(in all current sequences) at each time step. Currently these are only Poisson distributed but future
releases will change it to allow for other mutation methods.
SHM.branch.prob
Specifies the probability for a given sequence to undergo SHM events (thus, branching events)
This parameter corresponds to the distribution specified in "SHM.branch.prob". For "identical" only one value
should be supplied. For "uniform", a vector of length 3 should be specified corresponding to n,min,max respectively
(stats::runif(n, min = 0, max = 1)). For "exponential", a single value controlling the rate parameter (from stats::rexp()) should be supplied. For "lognorm"
a vector of length two should be supplied, with the first value corresponding to meanlog and the second
corresponding to sdlog (from stats::rlnorm). Similarly, for "normal" distribution, two values corresponding to
the mean and standard deviation (respectively) should be supplied.
SHM.branch.param
Describes the probability of undergoing SHM events. This parameter is responsible for
describing how likely each sequence will undergo branching events in the phylogeny. The following options are
possible: "identical", "uniform", "exponential" ("exp"), "lognormal" ("lognorm"), "normal" ("norm").
SHM.nuc.prob
Specifies the rate at which nucleotides change during speciation (SHM) events. This parameter
depends on the type of mutation specified by SHM.method. For both "poisson" and "data", the input value determines the probability
for each site to mutate (the whole sequence for "poisson" and the CDRs for "data"). For either "motif" or "wrc", the number of
mutations per speciation event should be specified. Note that these are not probabilities, but the number of mutations
that can occur (if the mutation is present in the sequence). If "all" is specified, the input should be a vector
where the first element controls the poisson style mutations, second controls the "data", third controls the "motif"
and fourth controls the "wrc".
species
Either "mus" for C57BL/6 germline genes or "hum" for human germline genes. These genes were
taking from IMGT. When more than one allele was present for a given gene, the first was used.
VDJ.branch.prob
The probabilty of a new VDJ recombination event of occuring. For the singleLineage function
this will result in a branching event at the site of the unmutated germline. For fullRepertoire function, this
will cause a new tree to begin.
proportion.sampled
Value ranging from 0 and 1 specifying the proportion of sequences to be sampled at each time point.
Specifiying 1 indicates that all sequences will be recovered at each time point, whereas 0.5 will sample half of the
sequences.
sample.time
Integer array indicating the time points at which sampling events should occur.
max.tree.num
Integer value describing maximum number of trees allowed
to generate the core sequences of the repertoire. Each of these trees is started
by an independent VDJ recombination event.