readCodelink {codelink} | R Documentation |
Read data exported as text by Codelink Software. It reads values (normalized by Codelink Software or not) flags and information about probes.
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, ...)
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. |
readCodelink returns an object of class "Codelink", whereas readCodelinkSet() returns a CodelinkSet object.
Diego Diez
## 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)