makePlaceholderMap: Make a placeholder map.
In gact/shmootl: QTL Analysis Utilities for Yeast

Make a placeholder map from the given combination of locus sequences, map unit, and map step size. If locus IDs are specified, the locus IDs of the placeholder map will be set from these. Otherwise, locus IDs are set to pseudomarker IDs or default marker IDs, according to whether map units are for a genetic or physical map, respectively.

1 2	makePlaceholderMap(locus.seqs, locus.ids = NULL, map.unit = "cM", step = 5)

`locus.seqs`	Sequences corresponding to individual loci.
`locus.ids`	Individual locus IDs.
`map.unit`	Map unit.
`step`	Map step size.

Locus sequences and locus IDs are assumed to be ordered. As in R/qtl, any sequence with too few loci is extended, to ensure that all sequences have enough loci.

The R/qtl map object - described in detail in Section 2.6 of Broman and Sen (2009) - comprises a nonempty list, each element of which contains two or more marker positions for a given chromosome. Each list element is named for its corresponding chromosome, while the names of each chromosome's marker position vector comprise the marker locus IDs.

Within shmootl, a map must represent either a genetic or a physical map. These are distinguished by the 'map.unit' attribute of an object, which can contain either genetic or physical map units.

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