batchPermScantwo: Run 'qtl::scantwo' on a batch of permuted 'cross' objects.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

Run qtl::scantwo on a batch of permuted cross objects.

Usage

batchPermScantwo(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 run. 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 scantwo.

Value

A scantwoperm list containing the results of the QTL scan for all permutations.

Author(s)

Thomas Walsh <[e-mail]>

Yue Hu

References

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

See Also

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

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