ct.keyCheck: Check compatibility of a sample key with a supplied...

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

Check compatibility of a sample key with a supplied ExpressionSet or similar object

Description

For many gCrisprTools functions, a sample key must be provided that specifies sample mapping to experimental groups. The sample key should be provided as a single, named factor whose names exactly correspond to the 'colnames()' of the 'ExpressionSet' containing the count data to be processed (or coercible as such). By convention, the first level corresponds to the control sample group.

This function checks whether the specified sample key is of the proper format and has properties consistent with the specified object.

Usage

ct.keyCheck(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 other matrix-like object with defined 'colnames()'.

Value

Invisibly, a properly formatted 'sampleKey'.

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.keyCheck(sk, es)

RussBainer/gCrisprTools documentation built on Nov. 5, 2022, 2:35 p.m.