inferTetradIndices: Infer sample tetrad indices.
In gact/shmootl: QTL Analysis Utilities for Yeast

Description Usage Arguments Value Sample IDs Tetradic Samples See Also

Infers tetrad indices of a set of samples from the given object. A character vector of sample IDs can be passed as the first argument, in which case the tetrad indices will be inferred, where possible, from the sample IDs themselves.

If a cross is the first argument, tetrad indices will be inferred from sample IDs, if present, or otherwise by comparison of sample genotypes.

inferTetradIndices(x)

## S3 method for class 'character'
inferTetradIndices(x)

## S3 method for class 'cross'
inferTetradIndices(x)

`x`	An R/qtl `cross` object, or a character vector of sample IDs.

Vector of sample tetrad indices inferred from the input object. Returns NULL if tetrad pattern could not be found.

A sample ID can be any valid item ID (see package overview). Duplicate sample IDs are permissible, but only if referring to replicate samples of the same strain. Different strains can have different numbers of replicates, but samples from a given strain must be in consecutive rows.

Sample IDs can be used to indicate tetrad membership, even in a cross object with some missing samples. In a tetradic dataset, sample IDs with a numeric suffix (e.g. 'FS101') are taken as segregant numbers and used to infer the tetrad to which each sample ID belongs, assuming that tetrads are labelled sequentially, with four samples per tetrad. Sample IDs can also have an alphanumeric suffix (e.g. 'FS01A'), where the numeric part is a tetrad number and the final letter (i.e. 'A', 'B', 'C', or 'D') identifies the individual tetrad member.

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