ct.targetSetEnrichment {gCrisprTools} | R Documentation

## Run a (limited) Pathway Enrichment Analysis on the results of a Crispr experiment.

### Description

This function enables some limited geneset enrichment-type analysis of data derived from a pooled Crispr screen using the PANTHER pathway database. Specifically, it identifies the set of targets significantly enriched or depleted in a `summaryDF` object returned from `ct.generateResults` and compares that set to the remaining targets in the screening library using a hypergeometric test.

Note that many Crispr gRNA libraries specifically target biased sets of genes, often focusing on genes involved in a particular pathway or encoding proteins with a shared biological property. Consequently, the enrichment results returned by this function represent the pathways containing genes disproportionately targeted *within the context of the screen*, and may or may not be informative of the underlying biology in question. This means that pathways not targeted by a Crispr library will obviously never be enriched within the positive target set regardless of their biological relevance, and pathways enriched within a focused library screen are similarly expected to partially reflect the composition of the library and other confounding issues (e.g., number of targets within a pathway). Analysts should therefore use this function with care. For example, it might be unsurprising to detect pathways related to histone modification within a screen employing a crispr library targeting epigenetic regulators.

This is a function that invokes the PANTHER.db Bioconductor library to extract a list of pathway mappings to be used in gene set enrichment tests. Specifically, the function returns a named list of pathways, where each element contains Entrez IDs. Users should not generally call this function directly as it is invoked internally by the higher-level `ct.PantherPathwayEnrichment()` function.

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 = "NoTarget",
      ...
    )

### Arguments

`summaryDF` | A dataframe summarizing the results of the screen, returned by the function `ct.generateResults`. Internally coerced via 'ct.simpleResult()'.
`targets` | A character vector containing the names of the targets to be tested; by default these are assumed to be 'geneID's, but specifying 'collapse=geneSymbol' enables setting on 'geneSymbol' by passing that value through to 'ct.simpleResult'.
`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 `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'.
`...` | Additional parameters to pass to 'ct.simpleResult'.
`pvalue.cutoff` | A gene-level p-value cutoff defining targets of interest within the screen. Note that this is a nominal p-value cutoff to preserve end-user flexibility.
`organism` | The species of the cell line used in the screen; currently only 'human' or 'mouse' are supported.
`db.cut` | Minimum number of genes annotated to a given to a pathway within the screen in order to consider it in the enrichment test.
`species` | The species of the cells used in the screen. Currently only 'human' or 'mouse' are supported.

### Value

A dataframe of enriched pathways.

A named list of pathways from `PANTHER.db`.

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, Steve Lianoglou

Russell Bainer, Steve Lianoglou.

Russell Bainer

### Examples

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

[Package gCrisprTools version 2.0.0 Index]