as.map: Convert object to 'map'.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

Convert object to map.

Usage

as.map(from, map.unit = NULL)

## S3 method for class 'data.frame'
as.map(from, map.unit = NULL)

## S3 method for class 'list'
as.map(from, map.unit = NULL)

## S3 method for class 'map'
as.map(from, map.unit = NULL)

## S3 method for class 'mapframe'
as.map(from, map.unit = NULL)

## S3 method for class 'scanone'
as.map(from, map.unit = NULL)

Arguments

from	Object containing map data.
map.unit	Explicitly sets 'map.unit' attribute. This must be specified if an object does not have an existing 'map.unit' attribute.

Value

An R/qtl map corresponding to the input object.

Map

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.

See Also

Other map utility functions: as.data.frame.mapframe, as.data.frame.map, as.mapframe, extractMarkers, extractPseudomarkers, findFlanking, findLoci, findMarkers, getMapSteps, getMapUnit, gmapframe, hasMapCSV, inMapOrder, inferMapStep, mapframe, mapsEqual, orderMap, readMapCSV, readMapHDF5, readMapframeCSV, setMapUnit, writeMapCSV, writeMapHDF5, writeMapframeCSV

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