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

In gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

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

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

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 Nov. 8, 2020, 8:17 p.m.