Description Usage Arguments References Examples
Creates cross with certain pattern of dependence across phenotypes.
1 2 3 4 5 6 7 | SimCrossCausal(n.ind, len, n.mar, beta, add.eff, dom.eff,
sig2.1 = 1, sig2.2 = 1, eq.spacing = FALSE,
cross.type = c("bc", "f2"), normalize = FALSE)
SimCrossIndep(n.ind, len, n.mar, beta, add.eff.1, dom.eff.1,
add.eff.h, dom.eff.h, sig2.1 = 1, sig2.2 = 1, sig2.h = 1,
eq.spacing = FALSE, cross.type = "f2", normalize = FALSE)
data(CMSTCross)
|
n.ind |
number of individuals to simulate |
len |
vector specifying the chromosome lengths (in cM) |
n.mar |
vector specifying the number of markers per chromosome |
beta |
causal effect (slope) of first phenotype on others |
add.eff, add.eff.1, add.eff.h |
additive genetic effect |
dom.eff, dom.eff.1, dom.eff.h |
dominance genetic effect |
sig2.1 |
residual variance for first phenotype |
sig2.2, sig2.h |
residual variance for all other phenotypes |
eq.spacing |
if |
cross.type |
type of cross ( |
normalize |
normalize values if |
Chaibub Neto E, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS, Causal model selection hypothesis tests in systems genetics. Genetics (in review).
1 2 3 4 5 6 7 8 9 10 11 | set.seed(987654321)
CMSTCross <- SimCrossCausal(n.ind = 100,
len = rep(100, 3), n.mar = 101,
beta = rep(0.5, 2), add.eff = 1, dom.eff = 0,
sig2.1 = 0.4, sig2.2 = 0.1, eq.spacing = FALSE,
cross.type = "bc", normalize = TRUE)
CMSTCross <- calc.genoprob(CMSTCross, step = 1)
## Not run:
save(CMSTCross, file = "CMSTCross.RData", compress = TRUE)
## End(Not run)
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