gl.sim.WF.table: Creates the reference table for running gl.sim.WF.run

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Creates the reference table for running gl.sim.WF.run

Description

This function creates a reference table to be used as input for the function gl.sim.WF.run. The created table has eight columns with the following information for each locus to be simulated:

• q - initial frequency.

• h - dominance coefficient.

• s - selection coefficient.

• c - recombination rate.

• loc_bp - chromosome location in base pairs.

• loc_cM - chromosome location in centiMorgans.

• chr_name - chromosome name.

• type - SNP type.

The reference table can be further modified as required.

See documentation and tutorial for a complete description of the simulations. These documents can be accessed at http://georges.biomatix.org/dartR

Usage

gl.sim.WF.table(
  file_var,
  x = NULL,
  file_targets_sel = NULL,
  file_r_map = NULL,
  interactive_vars = TRUE,
  seed = NULL,
  verbose = NULL,
  ...
)

Arguments

file_var	Path of the variables file 'ref_variables.csv' (see details) [required if interactive_vars = FALSE].
x	Name of the genlight object containing the SNP data to extract values for some simulation variables (see details) [default NULL].
file_targets_sel	Path of the file with the targets for selection (see details) [default NULL].
file_r_map	Path of the file with the recombination map (see details) [default NULL].
interactive_vars	Run a shiny app to input interactively the values of simulation variables [default TRUE].
seed	Set the seed for the simulations [default NULL].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].
...	Any variable and its value can be added separately within the function, will be changed over the input value supplied by the csv file. See tutorial.

Details

Values for the variables to create the reference table can be submitted into the function interactively through a Shiny app if interactive_vars = TRUE. Optionally, if interactive_vars = FALSE, values for variables can be submitted by using the csv file 'ref_variables.csv' which can be found by typing in the R console: system.file('extdata', 'ref_variables.csv', package ='dartR').

The values of the variables can be modified using the third column (“value”) of this file.

If a genlight object is used as input for some of the simulation variables, this function access the information stored in the slots x$position and x$chromosome.

Examples of the format required for the recombination map file and the targets for selection file can be found by typing in the R console:

• system.file('extdata', 'fly_recom_map.csv', package ='dartR')

• system.file('extdata', 'fly_targets_of_selection.csv', package ='dartR')

To show further information of the variables in interactive mode, it might be necessary to call first: 'library(shinyBS)' for the information to be displayed.

Value

Returns a list with the reference table used as input for the function gl.sim.WF.run and a table with the values variables used to create the reference table.

Author(s)

Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr

See Also

gl.sim.WF.run

Other simulation functions: gl.sim.WF.run(), gl.sim.create_dispersal()

Examples

ref_table <- gl.sim.WF.table(file_var=system.file('extdata', 
'ref_variables.csv', package = 'dartR'),interactive_vars = FALSE)
## Not run: 
#uncomment to run 
res_sim <- gl.sim.WF.run(file_var = system.file('extdata', 
'sim_variables.csv', package ='dartR'),ref_table=ref_table,
interactive_vars = FALSE)

## End(Not run)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.