makeScantwoThresholdObject: Make 'scantwo' threshold object.
In gact/shmootl: QTL Analysis Utilities for Yeast

Make scantwo threshold object.

1	makeScantwoThresholdObject(thresholds, phenotypes, alpha)

`thresholds`	Mapping or vector of `scantwo` LOD threshold values. If a mapping or named vector, threshold values are accessed by name, regardless of order. If an unnamed vector, threshold values are accessed by position, and are assumed to be in the same order as those of a `summary.scantwoperm` object.
`phenotypes`	Character vector of phenotypes for which the `scantwo` threshold object is being created.
`alpha`	Significance level (alpha) associated with the specified `scantwo` LOD thresholds.

A summary.scantwoperm object with the given scantwo thresholds at the specified significance level (alpha) for each LOD column. Because no permutations are used in generating the scantwo thresholds object, the returned object has attribute 'n.perm' containing the value 0.

Note that phenotype names are not included in the summary.scantwoperm object. This is a feature, not a bug, and is intended to match the behaviour of R/qtl in the case of a single significance level (alpha).

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