ct.targetSetEnrichment: Test Whether a Specified Target Set is Enriched Within a...

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

Description

This function takes in a resultsDF and a vector of targets (contained in the geneID column of resultsDF) and determines whether the specified targets are enriched within the set of all significantly altered targets. It does this by iteratively testing whether targets are more likely to be among the set of enriched or depleted targets at various significance thresholds using a hypergeometric test. Note that the returned Hypergeometric P-values are not corrected for multiple testing.

Returns a list detailing the targets used in the tests, and tables indicating the results of the hypergeometric test at various significance thresholds.

Usage

ct.targetSetEnrichment(summaryDF, targets, enrich = TRUE, ignore = NULL)

Arguments

summaryDF	A dataframe summarizing the results of the screen, returned by the function ct.generateResults.
targets	A character vector containing the names of the targets to be tested. Only targets contained in the geneID column of the provided summaryDF are considered.
enrich	Logical indicating whether to consider guides that are enriched (default) or depleted within the screen.
ignore	Optionally, a character vector containing elements of the geneID column of the provided summaryDF that should be ignored in the analysis (e.g., unassignable or nonfunctional targets, such as nontargeting controls). By default, this function omits targets with geneSymbol 'NoTarget'.

Value

A named list containing the tested target set and tables detailing the hypergeometric test results using various P-value and Q-value thresholds.

Author(s)

Russell Bainer

Examples

data(resultsDF)
tar <-  sample(unique(resultsDF$geneID), 20)
res <- ct.targetSetEnrichment(resultsDF, tar)

gCrisprTools documentation built on Nov. 8, 2020, 8:17 p.m.