shmootl: QTL Analysis Utilities for Yeast

Description Usage Arguments Details See Also

This function recodes the data in an R/qtl cross or genotype CSV file. Genotypes can be recoded by passing to the geno parameter a simple mapping of old to new genotypes. Alternatively, genotype data can be converted to enumerated genotypes by setting parameter enum.geno to TRUE.

1	recodeCSV(infile, outfile, geno = NULL, enum.geno = FALSE)

`infile`	Input CSV file path.
`outfile`	Output CSV file path.
`geno`	A simple `mapping` of old to new genotype symbols, with names containing existing genotype symbols, and elements containing their replacement values (incompatible with `enum.geno`).
`enum.geno`	Option indicating if genotype data should be recoded as enumerated genotypes (incompatible with `geno`).

Any mapping of old to new symbols must be complete and unambiguous. All existing values must be mapped to a new value, and data with different input values cannot have the same output value.

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