addGeneGrps: Function to load gene groups into maigesPreRaw object

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

Description

This function read a directory and read files containing the genes for specific gene groups. This files must have one gene per line. This function stores the gene groups read in the slot GeneGrps into objects of class maigesPreRaw.

Usage

addGeneGrps(data, folder="./", ext=".txt")

Arguments

data	object of maigesPreRaw class.
folder	char string specifying the directory of gene groups. The function tests the presence or not of the final bar.
ext	string giving the extension of the files, defaults to '.txt'. The function also tests the presence of the initial dot.

Details

If the data object already has gene groups with names equal to some someones that are been read, the groups with repeated names are not added. Warning messages are printed for every repeated group name.

The folder directory must contain only one file for each gene group of interest. These files must discriminate one gene per line. The identification of the genes must be done by one of the gene labels given by genemap (see loadData).

Value

This function returns another object of class maigesPreRaw, with the slot GeneGroups actualised.

Author(s)

Gustavo H. Esteves <[e-mail]>

See Also

maigesPreRaw, addPaths

Examples

## Don't run because you don't have the gene sets in a readable folder.
## Not run: 
gastro = addGeneGrps(gastro, folder="geneGrps", ext="txt")

## End(Not run)

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.