select_annotations: Annotations selection helper.

Description Usage Arguments Value

View source: R/AnnotationHelper.R

Description

Given a genome build identifier, creates a list of annotation databases which can be passed to the annotation functions.

Usage

1
select_annotations(genome.build)

Arguments

genome.build

The genome build to use for annotation.

Value

A list with the following elements:

TxDb

A TxDb of class AnnotationDBI providing informations about the genes of the selected build.

OrgDb

An OrgDb object for the selected species.

OrgDbStr

A character string representing the name of the OrgDb object.

BSGenome

A BSGenome object to retrieve DNA sequences.

KEGG

A cache of KEGG pathways, as returned by kegg.gsets from the gage library.

PWMBG

A PWMLogn background for motif enrichment of promoter regions.


ArnaudDroitLab/ef.utils documentation built on Nov. 3, 2018, 4:17 a.m.