View source: R/sim_phased_unphased.R
sim_phased_unphased | R Documentation |
Individual based simulation of the accumulation of junctions, returning phased and unphased data. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is returned.
sim_phased_unphased( pop_size = 100, freq_ancestor_1 = 0.5, total_runtime = 100, size_in_morgan = 1, markers = 100, time_points = -1, num_threads = 1, verbose = FALSE, record_true_junctions = FALSE, num_indiv_sampled = 10, coverage = 1, error_rate = 0 )
pop_size |
Population Size |
freq_ancestor_1 |
Frequency of ancestor 1 at t = 0 |
total_runtime |
Maximum time after which the simulation is to be stopped |
size_in_morgan |
Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome) |
markers |
If a single number is provided, the number is used as the total number of markers generated either randomly, or using a regular distribution (a regular distribution is chosen if the number is negative). If a vector is provided, that vector is used. |
time_points |
vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy). |
num_threads |
default is 1. -1 takes all available threads. |
verbose |
displays a progress bar |
record_true_junctions |
keep track of the true number of junctions? |
num_indiv_sampled |
the number of individuals sampled at each time point to be genotyped |
coverage |
fraction of markers that can be succesfully phased |
error_rate |
fraction of markers that are erroneously phased (e.g. swapped) |
a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
## Not run: sim_phased_unphased(pop_size = 100, freq_ancestor_1 = 0.5, total_runtime = 10, size_in_morgan = 1, markers = 10, time_points = c(0, 5, 10), num_threads = 1) ## End(Not run)
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