Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/scanone_shape.R
Runs genome scan on multivariate phenotypes with possible covariates
1 2 3 |
cross |
A cross object containing genotypes and some phenotypes |
chr |
(Optional) Names of chromosomes use for mapping |
pheno.col |
A numerical vector with column indicies in cross$pheno of the phenotypes to map or a vector containing their names. If missing, All but \"ID\" columns will be chosen as phenotypes. |
addcovar |
A dataframe with the additive covariates |
intcovar |
A dataframe with the interactive covariates - KEEP IT DEFAULT This argument and the followings except if state otherwise are not use so far They are there for direct |
n.perm |
Number of permutations |
perm.Xsp |
- KEEP IT DEFAULT, not use so far |
perm.strata |
- KEEP IT DEFAULT, not use so far |
n.cluster |
Number of clusters for parallelization of permutations |
test |
Multivariate test statistics: \'Pillai\', 'Hotelling.Lawley', \"Lik.ratio\", \"GoodallF\". Allows partial matching. |
formula |
Provides formula for the null model. Optional. |
Function takes a modified cross object with an additional class shape
obtained from update.cross
.
Additional covariates may be provided as supplementary arguments. Ordering of
observations in those additional covariates must match the new phenotypes.
Function returns a data.frame similar to the R/qtl scanone
function
with chromosome and cM positions in the two firsts columns and the $log_10$ of the p-value
for the multivariate phenotype. In the case of f2, there are three columns: full, purely additive and dominance models.
Nicolas Navarro
1 2 3 4 5 6 7 8 | data(fake.bc)
fake.bc <- calc.genoprob(fake.bc, step=2.5)
out <- scanoneShape(fake.bc, chr = 1, pheno.col = 1:2, addcovar = getsex(cross)$sex,
test = "Pillai")
plot(out)
-----------
Permutations
perm.scan <- scanoneShape(fake.bc, pheno.col=1:2, addcovar = getsex(cross)$sex, n.perm=1000, n.cluster=2)
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