batchPermScantwoF: Run 'funqtl::scantwoF' on batch of permuted 'cross' objects.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

Run funqtl::scantwoF on batch of permuted cross objects.

Usage

batchPermScantwoF(cross, pheno.col = NULL, n.cluster = 1, iseed = NULL,
  n.perm = 1000, perm.pheno = TRUE, perm.geno = FALSE, ...)

Arguments

cross	An R/qtl cross object.
pheno.col	Phenotype columns for which QTL analysis should be performed. If specified, phenotypes should contain measurements for consecutive values of the parameter of the function-valued trait (e.g. times). If no phenotypes are specified, all are used.
n.cluster	Number of nodes to request for parallel execution. Any number of processes can be requested with the argument n.cluster, but the number actually returned can be limited to the number of processes available. On a local computer, this limit is the number of physical cores in the computer. In a PBS batch system, the maximum number of processes will be set from the PBS node file.
iseed	Seed for random number generator.
n.perm	Number of permutations.
perm.pheno	Permute phenotype data.
perm.geno	Permute genotype data.
...	Additional keyword arguments passed to scantwoF.

Value

A scantwoperm list containing the results of scantwoF for all permutations. This has three elements - 'one', 'fullvadd', and 'fv1' - each containing a matrix of permutation results for one of three models: single QTL analysis, full-versus-additive QTL model, and full-versus-single QTL model, respectively.

References

Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890. (PubMed)

Kwak IY, Moore CR, Spalding EP, Broman KW (2014) A simple regression-based method to map quantitative trait loci underlying function-valued phenotypes. Genetics 197(4):1409-16. (PubMed)

See Also

Other scan utility functions: batchPermScanoneF, batchPermScanone, batchPermScantwo, batchPhenoScanone, batchPhenoScantwo, batchScan, nodePermScanoneF, nodePermScanone, nodePermScantwoF, nodePermScantwo, nodePhenoScanone, nodePhenoScantwo

gact/shmootl documentation built on Nov. 11, 2021, 6:23 p.m.