readCodelink: Read Codelink Bioarrays Data

In codelink: Manipulation of Codelink microarray 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)

codelink documentation built on Nov. 8, 2020, 8:19 p.m.