ct.GREATdb: Update a gene-centric msdb object for GREAT-style enrichment...

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

Update a gene-centric msdb object for GREAT-style enrichment analysis using a specified CRISPR annotation.

Description

Update a gene-centric 'GeneSetDb' object for GREAT-style enrichment analysis using a specified annotation.

Often, pooled screening libraries are constructed such that the gene targets of interest are associated with variable numbers of semi-independent screen signals (associated with, e.g., sets of alternative promoters or cis regulatory units). Such an arrangement is often unavoidable but produces to complications when performing gene set enrichent analyses. This function conforms a standard 'GeneSetDb' object to appropriately consider this form of ultiple testing during ontological enrichment analyses according to the GREAT strategy outlined by [McLean et al. (2009)](https://doi.org/10.1038/nbt.1630).

Operationally, this means that genewise sets in the provided object will be translated to the corresponding 'geneSymbol' sets provided in the annotation file.

Usage

ct.GREATdb(
  annotation,
  gsdb = sparrow::getMSigGeneSetDb(collection = c("h", "c2"), species = "human", id.type
    = "ensembl"),
  minsize = 10,
  ...
)

Arguments

annotation	an annotation object returned by ct.prepareAnnotation().
gsdb	A gene-centric GeneSetDb object to conform to the relevant peakwise dataset.
minsize	Minimum number of targets required to consider a geneset valid for analysis.
...	Additional arguments to be passed to 'ct.prepareAnnotation()'.

Value

A new GeneSetDb object with the features annotated genewise to pathways.

Examples

data(resultsDF)
data(ann)
gsdb <- ct.GREATdb(ann, gsdb = sparrow::getMSigGeneSetDb(collection = 'h', species = 'human', id.type = 'entrez'))
show(sparrow::featureIds(gsdb))

OscarBrock/gCrisprTools documentation built on Oct. 25, 2022, 7:29 a.m.