gsim {qgg} | R Documentation |
Genomic simulation
Description
Simulate Genotype and Phenotype Data
Usage
gsim(Glist = NULL, chr = 1, nt = 1, W = NULL, n = 1000, m = 1000, rsids = NULL)
Arguments
Glist |
A list of information about the genotype matrix. Default is 'NULL'. |
chr |
The chromosome(s) being used in the simulation. Default is 1. |
nt |
Number of traits. Default is 1. |
W |
Matrix of centered and scaled genotypes. Default is 'NULL'. |
n |
Number of individuals. Default is 1000. |
m |
Number of markers. Default is 1000. |
rsids |
A character vector of rsids. Default is 'NULL'. |
Details
This function simulates genotype and phenotype data based on the 'Glist', which is information about the genotype matrix.
Value
A list containing:
-
y
: Phenotypes. -
W
: Matrix of centered and scaled genotypes. -
e
: Errors. -
g
: Genotype effect. -
b0
,b1
: Coefficients. -
set0
,set1
: Selected markers. -
causal
: Causal markers.
Author(s)
Peter Soerensen
Examples
## Plink bed/bim/fam files
bedfiles <- system.file("extdata", paste0("sample_chr",1:2,".bed"), package = "qgg")
bimfiles <- system.file("extdata", paste0("sample_chr",1:2,".bim"), package = "qgg")
famfiles <- system.file("extdata", paste0("sample_chr",1:2,".fam"), package = "qgg")
# Summarize bed/bim/fam files
Glist <- gprep(study="Example", bedfiles=bedfiles, bimfiles=bimfiles, famfiles=famfiles)
# Simulate phenotype
sim <- gsim(Glist=Glist, chr=1, nt=1)
head(sim$y)
head(sim$e)
head(sim$causal)
[Package qgg version 1.1.2 Index]