loadData: Load cDNA microarray data tables

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

Description

This function loads a cDNA microarray dataset into a temporary maigesPreRaw object.

Usage

loadData(fileConf=paste(R.home(), "library/maiges/doc/gastro/load_gastro.conf", sep="/"))

Arguments

fileConf

string specifying a file name containing the parameters to load data. This file must contain all the information necessary to load the data, which are the following: dataDir: specify a folder name containing the data files to be loaded. The function tests the presence or not of the final bar. ext: string specifying the extension of the tables (if the sampleFile below don't contain this information). You don't need to put the dot onto string beginning, the function tests this automatically. sampleFile: string containing the file name with the descriptions of the biological samples hybridised, including the respective intensity data files. This file must be spreadsheet-like separated by tabs in a plain text format. The column fields 'File' and 'Ref' are mandatory (with exactly these names). The first one describes the files containing the numerical data and the second one describes the channel used to label the reference sample, must be 'green' or 'red' and they are not case sensitive. datasetId: string with a dataset identification. geneMap: as in sampleFile, this item is a character string giving a file name. This file must describe the genes on the slides. Also it must be a plain text spreadsheet-like separated by tabs. There are no mandatory field, but it is strongly recommended that you specify some fields containing gene names, genbank ID, cluster ID and gene annotations for a nice gene identification. headers: character string (in the R format) specifying the column fields from data files you want to load. skip: number of lines to be skipped in the numeric tables. sep: character that separates the fields on the numeric tables. gridR: number of print tip rows inside the slide. gridC: number of print tip columns inside the slide. printTipR: number of rows inside each print tip. printTipC: number of columns inside each print tip. You can see an example of this configuration file in RHOME/library/maiges/doc/gastro/load\_gastro.conf.

Details

This function takes the file name with initial arguments and load the dataset specified by this config file. It generate a maigesPreRaw object. During the process the function writes a file named load.out on your working folder, that is a log of the process, that you can check and verify if all was done correctly. Obviously, the parameters dataDir, sampleFile, geneMap, sep, gridR, gridC, printTipR, printTipC and headers must be specified. All other parameters may be specified as NULL and, if so, they are ignored. It is possible to specify any fields that you want in the headers parameter, but it is strongly recommended that you specify the fields of spot intensity and background for both channels and the filed giving quality weights for all spots.

Value

This function returns a maigesPreRaw object containing the dataset loaded.

Once an object of class maigesPreRaw was generated, you may use the functions addGeneGrps and addPaths to load informaation about gene groups and gene networks, respectively.

Author(s)

Gustavo H. Esteves <[e-mail]>

Examples

## Don't run because you don't have data tables.
## Not run: 
gastro = loadData(fileConf="load_gastro.conf")

## End(Not run)

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