ct.prepareAnnotation {gCrisprTools} | R Documentation

## Check and optionally subset an annotation file for use in a Crispr Screen

### Description

This function processes a supplied annotation object for use in a pooled screening experiment. Originally this was processed into something special, but now it essentially returns the original annotation object in which the geneSymbol column has been factorized. This is primarily used internally during a call to the `ct.generateResults()` function. Also performs some minor functionality checking.

### Usage

    ct.prepareAnnotation(ann, object = NULL, controls = TRUE,
      throw.error = TRUE)

### Arguments

`ann` | A `data.frame` containing an annotation object with gRNA-level information encoded as rows. The `row.names` attribute should correspond to the individual gRNAs, and it should at minimum contain columns named "geneID" and "geneSymbol" indicating the corresponding gRNA target gene ID and symbol, respectively.
`object` | If supplied, an object with `row.names` to be used to subset the supplied annotation frame for downstream analysis.
`controls` | The name of a value in the `geneSymbol` column of `ann` that corresponds to nontargeting control gRNAs. May also be supplied as a logical value, in which case the function will try to identify and format nontargeting guides.
`throw.error` | Logical indicating whether to throw an error when `controls` is `TRUE` but no nontargeting gRNAs are detected.

### Value

A new annotation data frame, usually with nontargeting controls and NA values reformatted to `NoTarget` (and `geneID` set to `'no_gid'`), and the "geneSymbol" column of `ann` factorized. If supplied with an `object`, the gRNAs not present in the `object` will be omitted.

### Author(s)

Russell Bainer

### Examples

    data('ann')
    data('es')
    es <- ct.filterReads(es)
    newann <- ct.prepareAnnotation(ann, es)

[Package gCrisprTools version 1.12.0 Index]