annotateDGEobj {DGEobj} R Documentation

### Description

Reads an annotation file containing key/value pairs or a named list and attaches them attributes to a DGEobj. If a file is used, it should be a text file containing key/value pairs separated by an equals sign. The keys argument specifies which keys we want to capture as attributes on the DGEobj.

### Usage

annotateDGEobj(dgeObj, annotations, keys = NULL)


### Arguments

 dgeObj A object of class DGEobj created by function initDGEobj() annotations Either a character string path to a file with annotations given as key/value pairs separated by an equal sign, or a named list of key/value pairs keys By default (value = NULL), all keys are read in and applied as DGEobj attributes. Use the keys argument to specify a specific list of keys to read from the file.

A DGEobj

### Examples

   MyDgeObj <- system.file("exampleObj.RDS", package = "DGEobj")

## Not run:
#using a text file file of key=value pairs
annotationFile <- "/location/to/myAnnotations.txt"
MyDgeObj <- annotateDGEobj(MyDgeObj, annotationFile)

#using a named list of key/values
annotations <- list(Title     = "Rat Liver Slices from Bile Duct Ligation animals",
Organism  = "Rat",
GeneModel = "Ensembl.R89")
MyDgeObj <- annotateDGEobj(MyDgeObj, annotations)

## End(Not run)



[Package DGEobj version 1.1.2 Index]