pVar: Retrieve Phenotypic Variable from Data

In renozao/xbioc: Extra Base Functions for Bioconductor

Description

This is a generic function to extract a phenotypic variable from data objects. It aims is to encompass variables that are directly defined as vectors or, for example, specified as a name that is looked up in the phenoData variables of an ExpressionSet object.

Usage

pVar(object, x, ...)

## S4 method for signature 'matrix'
pVar(object, x)

## S4 method for signature 'ExpressionSet'
pVar(object, x)

Arguments

object	an ExpressionSet object.
x	variable as an atomic vector or as a string corresponding to the name of a phenotypic variable to be looked up in phenData(object).

Methods (by class)

• matrix: simply returns x, after checking that it has the same length as the number of columns in x.

• ExpressionSet: either return x or the phenotypic variable pData(object)[[x]] if it exists.

renozao/xbioc documentation built on Sept. 3, 2020, 1:13 a.m.