readCodelink {codelink} | R Documentation

## Read Codelink Bioarrays Data

### Description

Read data exported as text by Codelink Software. It reads values (normalized by Codelink Software or not) flags and information about probes.

### Usage

    readCodelink(files = list.files(pattern = "TXT"), sample.name =
                     NULL, flag, flag.weights, type.weights, dec = NULL,
                     type = "Spot", preserve = FALSE, verbose = 2,
                     file.type = "Codelink", check = TRUE, fix = FALSE, old
                     = FALSE)
    readCodelinkSet(filename, path, phenoData = NULL, ...)

### Arguments

`files` | list of files to read.
`sample.name` | vector of same length as files with sample names.
`flag` | list with values to assign based on Flag quality values.
`flag.weights` | weights assigned to each probe flag.
`type.weights` | weights assigned to each probe type.
`dec` | character indicating the decimal character used in the files.
`type` | character indicating which base value to read from files.
`preserve` | logical, if TRUE Bkgd\_stdev slot is not removed (if present).
`verbose` | numerical, set the level of information. Level 2 set as old behaviour. Level > 2 output some debug info.
`file.type` | exported file type, currently Codelink or XLS file formats supported.
`check` | logical, check for probe order consistency.
`fix` | logical, try to fix probe order consistency.
`old` | logical, whether NA is assigned to intensities based on flags.
`filename` | list of files.
`path` | path to the files.
`phenoData` | phenoData object with sample information.
`...` | further arguments to be passed.

### Value

readCodelink returns an object of class "Codelink", whereas readCodelinkSet() returns a CodelinkSet object.

### Author(s)

Diego Diez

### Examples

    ## Not run:
    	# specify a different one.
        f <- list.files(pattern = "TXT")
        codset <- readCodelinkSet(filename = f)

    	# read a targets file with phenotypic information
        # including sample names, file names and sample groups.
        pdata = read.AnnotationDataFrame("targets.txt")
        codset = readCodelinkSet(pdata$FileNames, phenoData=pdata)

        data(codset)

    ## End(Not run)

[Package codelink version 1.50.0 Index]