View CDFs of the ranked gRNAs or Targets present in a crispr screen

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Description

This function generates a plot relating the cumulative proportion of reads in each sample of a crispr screen to the abundance rank of the underlying guides (or Targets). The purpose of this algorithm is to detect potential distortions in the library composition that might not be properly controlled by sample normalization (see also: ct.stackedGuides()).

Usage

1
ct.guideCDF(eset, sampleKey = NULL, plotType = "gRNA", annotation = NULL)

Arguments

eset

An ExpressionSet object containing, at minimum, a matrix of gRNA abundances extractable with the exprs() function.

sampleKey

An optional sample key, supplied as an ordered factor linking the samples to experimental variables. The names attribute should exactly match those present in eset, and the control set is assumed to be the first level.

plotType

A string indicating whether the individual guides should be displayed ("gRNA"), or if they should be aggregated into target-level estimates ("Target") according to the geneSymbol column in the annotation object.

annotation

An optional data.frame containing an annotation object to be used to aggregate the guides into targets. gRNAs are annotated by row, and must minimally contain a column geneSymbol indicating the target elements.

Value

A CDF plot displaying the appropriate CDF curves on the default device.

Author(s)

Russell Bainer

Examples

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