scanoneShape: scanoneShape

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/scanone_shape.R

Description

Runs genome scan on multivariate phenotypes with possible covariates

Usage

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scanoneShape(cross, chr, pheno.col, addcovar = NULL, intcovar = NULL,
  n.perm, perm.Xsp = FALSE, perm.strata = NULL, n.cluster = 1,
  test = c("Pillai", "Hotelling.Lawley", "Lik.ratio", "GoodallF"), formula)

Arguments

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.

Details

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.

Value

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.

Author(s)

Nicolas Navarro

See Also

scanone

Examples

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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)

nnavarro/shapeQTL documentation built on April 30, 2021, 12:10 p.m.