ct.topTargets {gCrisprTools} | R Documentation

## 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

    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 `geneSymbol`s 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 `geneSymbol`s 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

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

    ct.topTargets(fit, resultsDF, ann)

[Package gCrisprTools version 1.20.0 Index]