batchPermScanone: Run 'qtl::scanone' on a batch of permuted 'cross' objects.
In gact/shmootl: QTL Analysis Utilities for Yeast

Description Usage Arguments Value References See Also

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

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batchPermScanone(cross, pheno.col = NULL, n.cluster = 1, iseed = NULL,
  n.perm = 1000, perm.pheno = TRUE, perm.geno = FALSE,
  perm.type = c("max", "bins"), ...)

`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.
`perm.type`	Type of permutation data (see below).
`...`	Additional keyword arguments passed to `scanone`.

If perm.type is set to 'max', a regular scanoneperm object is returned, containing the maximum LOD values from the given permutations. If perm.type is set to 'bins', a scanonebins array is returned. Each row of this array corresponds to a permutation, each array column corresponds to a bin spanning an interval of LOD values, and each slice corresponds to a LOD column. Each element contains the number of loci in the given bin interval for that LOD column in that permutation.

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

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