annotateDGEobj {DGEobj}R Documentation

Add annotations

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.

Value

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)

## End(Not run)
   #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)


[Package DGEobj version 1.0.3 Index]