SimCrossCausal {qtlcmst} | R Documentation |
Creates cross with certain pattern of dependence across phenotypes.
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) 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 |
additive genetic effect |
dom.eff |
dominance genetic effect |
sig2.1 |
residual variance for first phenotype |
sig2.2 |
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).
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)