annotateRanges_great: Annotate profileplyr ranges to genes using rGREAT

In RockefellerUniversity/profileplyr: Visualization and annotation of read signal over genomic ranges with profileplyr

Annotate profileplyr ranges to genes using rGREAT

Description

The ranges from the deepTools matrix will be subset based on whether they overlap with specified annotated regions related to a user defined gene list.

Usage

annotateRanges_great(object = "profileplyr", species = "character", ...)

## S4 method for signature 'profileplyr'
annotateRanges_great(object = "profileplyr", species = "character", ...)

Arguments

object	A profileplyr object
species	GREAT accepts "hg19", "mm10", "mm9", "danRer7" (zebrafish)
...	pass to submitGreatJob

Details

tbd

Value

A profileplyr object

Methods (by class)

• annotateRanges_great(profileplyr): Annotate profileplyr ranges to genes using rGREAT

Examples

library(SummarizedExperiment)
example <- system.file("extdata", "example_deepTools_MAT", package = "profileplyr") 
object <- import_deepToolsMat(example)
object <- object[1:5, , ] 

# annotate ranges with genes using GREAT with following command:
annotateRanges_great(object, species = "mm10")

RockefellerUniversity/profileplyr documentation built on Jan. 28, 2023, 10:09 a.m.