inferStrainIndices: Infer sample strain indices.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

Infers strain indices of a set of samples from the given object. A character vector of sample IDs can be passed as an argument, in which case the strain indices will be inferred from each set of identical consecutive sample IDs. If a cross object is passed as an argument, strain indices will be inferred from sample IDs, if present. Otherwise, strain indices are inferred from each set of identical consecutive sample genotypes.

Usage

inferStrainIndices(x)

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

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

Arguments

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

Value

Vector of sample strain indices inferred from the input object.

Sample IDs

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.

See Also

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

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