annotateRanges_great {profileplyr} | R Documentation

## 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)

- `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")

[Package profileplyr version 1.2.0 Index]