ct.signalSummary: Generate a Figure Summarizing Overall Signal for One or More...
In gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Description Usage Arguments Value Author(s) Examples

Given one or more targets of interest, this function generates a summary image contextualizing the corresponding signals within the contest of the provided contrast. This takes the form of an annotated ranking curve of target-level signals, supplemented with horizontal Q-value cutoffs and an inset volcano plot of gRNA behavior.

Limited annotation is provided for the specified targets using the following logic:

- If a character vector is provided, up to five targets are annotated; longer lists are highlighted without specifying individual elements. - If a list is provided, the 'names' element is used as the annotation. This is similarly constrained to a total of 5 annotated elements.

ct.signalSummary(
  summaryDF,
  targets,
  direction = c("enrich", "deplete"),
  callout = FALSE
)

`summaryDF`	A dataframe summarizing the results of the screen, returned by the function `ct.generateResults`.
`targets`	A list or character vector containing the names of the targets to be displayed. Only targets contained in the `geneSymbol` column of the provided `summaryDF` are considered. Plotting priority (e.g., the points to plot last in the case of overlapping signals) is given to earlier elements in the list.
`direction`	Should enrichment or depletion be considered? Must be one of `"enrich"` or `"deplete"`.
`callout`	Logical indicating whether lines should be plotted indicating individual gene sets to augment the point highlighting.

A summary plot on the current device.

Russell Bainer

data('resultsDF')
ct.signalSummary(resultsDF, list('CandidateA' = 'Target229', 'Pathway3' = resultsDF$geneSymbol[c(42,116,1138,5508)]), 'enrich')
data('es')
data('ann')
data('fit')

ct.GCbias(es, ann)
ct.GCbias(fit, ann)