importAnnotationHub-methods: *importAnnotationHub*

In BrendelGroup/TSRchitect: Promoter identification from large-scale TSS profiling data

Description

imports an annotation directly from AnnotationHub and attaches it to the tssObject

Usage

importAnnotationHub(experimentName, provider, annotType, species, annotID)

## S4 method for signature 'tssObject,character,character,character,character'
importAnnotationHub(experimentName, provider, annotType, species, annotID)

Arguments

experimentName	- an S4 object of class tssObject that contains information about the experiment
provider	- 'character' the source of the annotation in AnnotationHub (e.g. 'gencode')
annotType	- 'character' the format of the annotationHub annotation to be imported. Using 'gff' will find annotations in both gff or gff3 formats
species	- 'character' the species identifier in AnnotationHub (e.g. 'human')
annotID	- 'character' the AnnotationHub identifier to be retrieved

Value

fills the slot @annotation in the returned tssObject with an AnnotationHub record. The record retrieved must be an object of class GRanges.

Note

An example similar to the one provided can be found in the vignette (/inst/doc/TSRchitect.Rmd)

Please consult the available records in AnnotationHub beforehand using AnnotationHub-class

BrendelGroup/TSRchitect documentation built on March 3, 2021, 1:45 a.m.