readpDataSlides {arrayMagic}R Documentation

Reads the description of all slides or channels

Description

The function reads the slideDescriptionFile, which contains all information row-wise for each slide/microarray or for each channel in a tab-deliminated text file. The file is read up to the first line containing solely "white space".

Usage

readpDataSlides(slideDescriptionFile = "slideDescription.txt", loadPath = ".", deleteBlanks = TRUE, verbose = TRUE)

Arguments

slideDescriptionFile character string; required; default "slideDescription.txt". The first line of the file must contain all column names, in particular the column named "fileName" which contains image analyis result file names and possibly additionally a column which contains the slide names; cf. the arguments fileNameColumn and slideNameColumn of readIntensities. Note: Column names must not contain underlines or spaces.
loadPath character string; required; default: ".". The path is used to load the slideDescriptionFile; note: "." refers to the working directory.
deleteBlanks logical; required; default: TRUE. Any blank character is removed from the text body of the slideDescriptionFile. Thus no item/name should contain spaces.
verbose logical; required; default: TRUE

Value

data.frame

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

readIntensities, processArrayData

Examples

       LOADPATH <- file.path(.path.package("arrayMagic"), "extdata")
        SLIDEDESCRIPTIONFILE <- "slideDescription"
  
        resultObject <- readpDataSlides(
                             loadPath=LOADPATH, 
                             slideDescriptionFile=SLIDEDESCRIPTIONFILE
                  )
 

[Package arrayMagic version 1.10.0 Index]