ct.expandAnnotation: Expand an annotation object to allow annotations of reagents...

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

Expand an annotation object to allow annotations of reagents to multiple targets

Description

This function takes a gCrisprTools annotation object and expands it to allow 1:many mappings of reagents. This mostly is used for internal processing, and users should interact with the wrapper functions that call it (e.g., 'ct.generateResults').

Libraries targeting ambiguous biological elements (e.g., alternative promoters to a gene where the boundaries between elements is contested) may contain reagents that are plausibly annotated to a finite set of possible targets. To accomodate this, users may supply an alternative reagent annotation in the form of a named list of vectors, where the names correspond to reagent 'ID's in the annotation object and each list element corresponds something coercible to a to a character vector of associated targets that will ultimately be assembled into the 'geneSymbol' column of the annotation object. It is assumed that the 'geneID' values are assigned unambiguously to the reagents, and are passed through directly.

Usage

ct.expandAnnotation(ann, alt.annotation)

Arguments

ann	A data.frame containing an annotation object with gRNA-level information encoded as rows, typically produced by 'ct.prepareAnnotation'. The 'ID' column should correspond to the individual reagent identifiers.
alt.annotation	A named list of character vectors, which should be named identically to a value in the 'ID' column of the supplied annotation object. The values in the character vectors will eventually form the 'geneSymbol' column of the annotation file.

Value

A new annotation data frame, expanded as described above.

Author(s)

Russell Bainer

Examples

data('ann')
alt.annotation <- list('Target2089_b' = c('foo', 'bar'), 'Target2089_c' = 'foo', 'Target2089_a' = 'bar')
ct.expandAnnotation(ann, alt.annotation)

RussBainer/gCrisprTools documentation built on Nov. 5, 2022, 2:35 p.m.