readMapCSV: Read 'map' from a CSV file.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

This function reads a yeast cross genetic or physical map from any R/qtl CSV file that contains map data, whether that file contains a map table, genotype data, or a full cross.

Usage

readMapCSV(infile, require.mapunit = TRUE)

Arguments

infile	Input CSV file path.
require.mapunit	Require map unit information.

Details

By default, the input map must include map unit information (e.g. 'cM', 'bp'). In the case of a map table file, this information can be indicated in the map headings (e.g. 'pos (cM)') or in the map positions (e.g. '47 cM'). For a cross or genotype file, map units should be included with map positions.

To read an input file without requiring map units, set parameter require.mapunit to FALSE. If map units are not required and not found, map positions are assumed to be in centiMorgans.

Value

An R/qtl map object.

See Also

Other CSV functions: hasMapCSV, readCovarCSV, readCrossCSV, readGenoCSV, readMapframeCSV, readPhenoCSV, recodeCSV, sniffCSV, writeCrossCSV, writeGenoCSV, writeMapCSV, writeMapframeCSV, writePhenoCSV

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

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