readCrossCSV: Read yeast 'cross' from a CSV file.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

This function reads yeast cross data from an R/qtl CSV file and returns an R/qtl cross object. The returned cross has an attribute 'info' of type CrossInfo, which contains information about the input cross.

Usage

readCrossCSV(infile, error.prob = 1e-04, map.function = c("haldane",
  "kosambi", "c-f", "morgan"), require.mapunit = TRUE)

Arguments

infile	Input CSV file path.
error.prob	Genotyping error rate.
map.function	Genetic map function.
require.mapunit	Require map unit information in map positions.

Details

If a genetic map is not present in the input file, this is estimated when loading the cross. In such cases, parameters error.prob and map.function are passed to R/qtl for map estimation.

By default, any genetic map positions must include map units (i.e. 'cM'). To read a cross 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 cross object with an attribute 'info' of type CrossInfo.

See Also

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

Other cross object functions: crossesEqual, getIdColIndex, getPhenoColIndices, hasTimeSeriesPhenotypes, inferStrainIndices, inferTetradIndices, inferTimeStep, interpTimeSeries, padTimeSeries, permCross, permIndices, pull.alleles, pull.chr, pull.crosstype, pull.ind, readCrossHDF5, writeCrossCSV, writeCrossHDF5

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