Hi Assa,
First off, please don't cross-post. This is really an R-help question,
as it is about the R language rather than a specific BioC package.
Assa Yeroslaviz wrote:
dear all,
I have a problem with a masked object in a package we created here.
we make a package for a workflow of internal analysis of microarray data.
to create the package we used:
install.packages(pkgs="affyAnalysis", repos=NULL)
R CMD INSTALL affyAnalysis
Erzeuge Verzeichnisse ...
Erzeuge DESCRIPTION ...
Erzeuge NAMESPACE ...
Erzeuge Read-and-delete-me ...
Kopiere Code-Dateien ...
Erzeuge Hilfedateien ...
Fertig.
one of the classes in the package is a S3 packge and has the name
"preprocess".
using the package require various packages. one of them is affyPLM, which
also have a S3 class named preprocess.
Each time I'm using the program i get the message:
library(affyPLM)
Lade nötiges Paket: affy
Lade nötiges Paket: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Lade nötiges Paket: gcrma
Lade nötiges Paket: preprocessCore
Attache Paket: 'affyPLM'
The following object(s) are masked from package:affyAnalysis :
preprocess
The following object(s) are masked from package:stats :
resid,
residuals,
weights
The preprocess command in the affyPLM package needs an affybatch object to
work with.
our preprocess is as such definiert:
preprocess <- function(x,...) UseMethod("preprocessExpData")
preprocessExpData.expData <- function(data){
require("vsn")
data <- list(ExpressionSet=vsnrma(data$AffyBatch),
baseDir=data$baseDir,experimentName=data$experimentName,
pData=pData(data$AffyBatch))
class(data) <- c("expSet","list")
return(data)
}
when using the workflow we have and coming to the point of preprocesswe get
the following error message:
ex <- preprocess(ed)
Fehler in preprocess(ed) :
argument is expData threestep requires AffyBatch argument is list
threestep requires AffyBatch
I would like to know if there is a way of using both preprocess commands
without the need to rename ours. They both use different object structure as
an input and as far I understand the adventages of OOP in R it should be
able to recognize this differences, but how?
You need to take advantage of the namespace mechanisms available to you.
The affyPLM package has a NAMESPACE file, and your package should as
well. If you need preprocess from affyPLM, you can simply call it as
affyPLM::preprocess
which will ensure that you get the function you want. You can do the
same with the function from your package (affyAnalysis::preprocess).
Best,
Jim
Thans in advance for your help
Assa
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