Description Usage Arguments Details Value Author(s) Examples
Main process of simulation for phenotypes
1 2 3 4 5 |
sim.pars |
a prepared list containing the parameters settings for simulation or a file of parameters settings.
Please set your own parameters
following the same structure as the object List format: please follow the example of the object File format: please follow the example of the
Similar meanings for "[P2mean]", "[P2main]", "[P2epistasis]", and so on. |
fgeno |
file to read genotype information from or pre-read data.frame
with that information (matching the output format of
|
ftype |
genotype file format, it accepts three options:
For "plink", |
fwrite |
logical. Write out file (simulated data) or not. If TRUE (default), simulated phenotypes will be written, respectively. |
fphename |
filename of the phnotype(s). Default is "simu.pheno". |
fusepar |
filename of the setting for simulation (for recording). Default is "usedpars.txt". |
seed |
an integer used for set.seed(). Default is NA. |
Dskim |
the coefficient of linkage disequilibrium. Default is 0 (no LD). |
noise.var |
variance for random noise. Default is 1. Note that this
is overridden by the heritability setting in the
simulation parameter file. If heritability is
given in parameter file then |
pattern |
ignore pattern for detecting the phenotype index from the parameter names. Default is "[[:alpha:]]+" which means letters. |
plink.path |
path of plink executable. Only needed when the |
genetic.model |
a string show the genetic model to use for simulation. Default is "epistasis". |
... |
not used. |
further discussion on pattern
a data.frame with the simulated phenotype(s) where the column(s) refer to different phenotype(s) and rows to individuals.
Beibei Jiang beibei_jiang@psych.mpg.de and Benno Pütz puetz@psych.mpg.de
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | #### file path of example
# simulation parameters:
fpar.path <- system.file("extdata", "simupars.txt", package="SimPhe")
# genotype file: rows are individuals and columns are SNPs
fgeno.path <- system.file("extdata", "10SNP.txt", package="SimPhe")
#### instead of a parameter file, prepared list like genepars also works
genepars
#### simulate phenotype(s)
phe <- sim.phe(sim.pars = fpar.path, fgeno = fgeno.path, ftype = "snp.head", fwrite = FALSE)
# or
phe <- sim.phe(sim.pars = genepars, fgeno = fgeno.path, ftype = "snp.head", fwrite = FALSE)
# the simulated phenotype(s)
str(phe)
head(phe)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.