readCelFile {Starr} | R Documentation |
Function to read the raw intensities of the perfect match probes (PM) of Affymetrix CEL files into an ExpressionSet. This function is used to read one-color data. For two-color data use the functions from the Ringo package.
readCelFile(bpmap, cel_files, names, type, experimentData=NULL, featureData=T, log.it=T, phenodata=NULL)
bpmap |
Either a list, created by the function readBpmap() from the affy package, or the path to the bpmap file. |
cel_files |
a character vector, specifying the path to the CEL files |
names |
a character vector, containing the names of the experiments |
type |
a character vector, containing the type of experiment, e.g. "IP" for an Immunoprecipitation, or "CONTROL" for a control or reference experiment was done |
experimentData |
This must be an object of type MIAME, which details information about e.g., the investigator or lab where the experiment was done, an overall title, and other notes |
featureData |
If TRUE, a featureData object is added to the ExpressionSet, containing information about the chromosome, position in the genome and sequence of the features |
log.it |
If TRUE, logged intesities are read |
phenodata |
data.frame, containing columns name, type, CEL. |
Returns raw intensity values in form of an ExpressionSet with additional information:
assayData |
This object contains the measured probe intensities. |
phenoData |
contains further description of the experiments, such as names or type |
featureData |
containing information about the chromosome, position in the genome and sequence of the features |
experimentData |
details information about e.g., the investigator or lab where the experiment was done |
Benedikt Zacher zacher@lmb.uni-muenchen.de
readCelIntensities
, xy2indices
## # dataPath <- system.file("extdata", package="Starr") # bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap")) # cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"), # file.path(dataPath,"Rpb3_IP2_chr1.cel")) # names <- c("rpb3_1", "wt_1","rpb3_2") # type <- c("IP", "CONTROL", "IP") # rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=TRUE, log.it=TRUE)