ct.inputCheck: Check compatibility of a sample key with a supplied object

Description Usage Arguments Value Author(s) Examples

View source: R/fileutilities.R

Description

For many gCrisprTools functions, a sample key must be provided that specifies sample mapping to experimental groups and specifies which of these contains control samples. This function checks whether the specified sample key is of the proper format and has properties consistent matching the specified object.

Usage

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ct.inputCheck(sampleKey, object)

Arguments

sampleKey

A named factor, where the levels indicate the experimental replicate groups and the names match the colnames of the expression matrix contained in object. The first level should correspond to the control samples, but obviously there is no way to algorithmically control this.

object

An ExpressionSet, EList, or matrix.

Value

A logical indicating whether the objects are compatible.

Author(s)

Russell Bainer

Examples

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data('es')
library(limma)
library(Biobase)

#Build the sample key
sk <- relevel(as.factor(pData(es)$TREATMENT_NAME), "ControlReference")
names(sk) <- row.names(pData(es))
ct.inputCheck(sk, es)

gCrisprTools documentation built on May 31, 2017, 11:42 a.m.