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

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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

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## 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)

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