getPhenoColIndices: Get phenotype column indices.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

Get the indices of the phenotype columns in the given object. In a data.frame, phenotype columns are those columns that do not have reserved phenotype headings (e.g. 'ID'). In a cross object, these are the corresponding columns of the phenotype data.frame.

Usage

getPhenoColIndices(x, pheno.col = NULL)

## S3 method for class 'cross'
getPhenoColIndices(x, pheno.col = NULL)

## S3 method for class 'data.frame'
getPhenoColIndices(x, pheno.col = NULL)

Arguments

x	A data.frame containing phenotype data, or an R/qtl cross object containing such a data.frame.
pheno.col	Vector indicating the phenotype indices to return. This can be an integer vector of phenotype column indices with respect to the columns of the data.frame (which may or may not be within a cross object), or a character vector that contains phenotype IDs or their syntactically valid names. If none are specified, all phenotype column indices are returned.

Value

Phenotype column indices.

See Also

Other cross object functions: crossesEqual, getIdColIndex, hasTimeSeriesPhenotypes, inferStrainIndices, 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.