readMapframeCSV: Read 'mapframe' from a CSV file.

Description Usage Arguments Details Value See Also

View source: R/csv.R

Description

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

Usage

1
readMapframeCSV(infile, require.mapunit = TRUE)

Arguments

infile

Input CSV file path.

require.mapunit

Require map unit information.

Details

By default, the input mapframe 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

A mapframe object.

See Also

Other CSV functions: hasMapCSV, readCovarCSV, readCrossCSV, readGenoCSV, readMapCSV, 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, readMapCSV, readMapHDF5, setMapUnit, writeMapCSV, writeMapHDF5, writeMapframeCSV


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