Simulate sequence data for a pedigree
sim_seq(ped_file, founder_genos, SNV_map, chrom_map, RV_marker,
burn_in = 1000, gamma_params = c(2.63, 2.63/0.5))Data frame. A single pedigree. Must match format of pedigree simulated by sim_RVped
Dataframe. A dataframe with rows corresponding to founders, and columns corresponding to markers. Markers must be listed in same order as SNV_map.
Data frame. A data frame that catalogs the SNVs in haplos. If the read_slim function was used to import SLiM data to R, the data frame Mutations is of the proper format for SNV_map. However, users must add the variable is_CRV to this data frame, see details.
Data.frame. A data.frame consisting of three columns: column 1 contains the chromosome numbers, column 2 start postion of chromosome (in cM), column 3 end position of chromosome (in cM).
character. The marker name of the RV locus.
Numeric. The "burn-in" distance in centiMorgan, as defined by Voorrips and Maliepaard (2012), which is required before simulating the location of the first chiasmata with interference. By default, burn_in = 1000.
The burn in distance in cM. By default, burn_in = 1000.
Numeric list of length 2. The respective shape and rate parameters of the gamma distribution used to simulate distance between chiasmata. By default, gamma _params = c(2.63, 2*2.63), as discussed in Voorrips and Maliepaard (2012).
offspring_sequences