nodePermScanone: Run 'qtl::scanone' on a single permuted 'cross' object.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

Run qtl::scanone on a single permuted cross object.

Usage

nodePermScanone(perm.id, cross, pheno.col = NULL, perm.pheno = TRUE,
  perm.geno = FALSE, perm.type = c("max", "bins"), ...)

Arguments

perm.id	Permutation index.
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.
perm.pheno	Permute phenotype data.
perm.geno	Permute genotype data.
perm.type	Type of permutation data to return (see below).
...	Additional keyword arguments passed to scanone.

Value

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

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, batchPermScantwo, batchPhenoScanone, batchPhenoScantwo, batchScan, nodePermScanoneF, nodePermScantwoF, nodePermScantwo, nodePhenoScanone, nodePhenoScantwo

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