Display the log2 fold change estimates and associated standard deviations of the guides targeting the top candidates in a crispr screen

Description

This is a function for displaying candidates from a crispr screen, using the information summarized in the corresponding fit and the output from ct.generateResults(). The fold change and standard deviation estimates for each gRNA associated with each target (extracted from the coefficients and stdev.unscaled slot of fit) are plotted on the y axis. Targets are selected on the basis of their gene-level enrichment or depletion P-values; in the case of ties, they are ranked on the basis of their corresponding Rho statistics.

Usage

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ct.topTargets(fit, summaryDF, annotation, targets = 10, enrich = TRUE,
  contrast.term = NULL)

Arguments

fit

An object of class MArrayLM containing, at minimum, a coefficents slot with coefficients from the comparison, and a stdev.unscaled slot with the corresponding standard deviation of the coefficent estimates. The row.names attribute should ideally match that which is found in annotation.

summaryDF

A data.frame summarizing the results of the screen, returned by the function ct.generateResults.

annotation

An annotation object for the experiment. gRNAs are annotated by row, and must minimally contain a column geneSymbol.

targets

Either the number of top targets to display, or a list of geneSymbols contained in the geneSymbol slot of the annotation object.

enrich

Logical indicating whether to display guides that are enriched (default) or depleted within the screen. If a vector of geneSymbols is specified, this controls the left-t0-right ordering of the corresponding gRNAs.

contrast.term

If a fit object with multiple coefficients is passed in, a string indiating the coefficient of interest.

Value

An image on the default device indicating each gRNA's log2 fold change and the unscaled standard deviation of the effect estimate, derived from the MArrayLM object.

Author(s)

Russell Bainer

Examples

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data('fit')
data('resultsDF')
data('ann')

ct.topTargets(fit, resultsDF, ann) 

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