Hi Tim,
On 02/26/2013 02:01 PM, Tim Triche, Jr. wrote:
It seems like the best way to write an email around these parts is using R
code, so here goes. I'm just wondering why a coercion that I define for
DataFrame -> data.frame doesn't automatically get used in practice.
library(Biobase)
library(GEOquery)
library(GenomicRanges)
## download a dataset which will become a SummarizedExperiment
##
gset <- getGEO("GSE41826") ## GSEMatrix seems to hose it
if (length(gset) > 1) idx <- grep("GPL13534", attr(gset, "names"))
else idx <- 1 ## a kludge, for dealing with SuperSeries entries
gset <- gset[[idx]]
sampleNames(gset) <- gset$title
## turn it into a SummarizedExperiment so I can call DMRs
if(require(regulatoR))
sortedBrainCells <- as(gset, 'SummarizedExperiment')
## the above could maybe become a generic for GEOquery... !?
## massage some covariates
sortedBrainCells$sex <-
as.factor(sub('Sex: ', '', sortedBrainCells$characteristics_ch1.2))
sortedBrainCells$race <-
as.factor(sub('race: ', '', sortedBrainCells$characteristics_ch1.3))
sortedBrainCells$age <-
as.numeric(sub('age: ', '', sortedBrainCells$characteristics_ch1.4))
## now the part that is bugging me: why won't R coerce automatically?
##
## define a coercion for DataFrame to data.frame:
setAs("DataFrame", "data.frame", function(from) as.data.frame(from))
##
## try to assemble a model.matrix
model.matrix(~ age + race + sex, data=colData(sortedBrainCells))
##
## D'OH!
##
## Error in as.data.frame.default(data, optional = TRUE) :
## cannot coerce class "structure("DataFrame", package = "IRanges")" to a
data.frame
What seems to be called internally is as.data.frame.default, and
of course as.data.frame.default as no idea how to convert a DataFrame
into a data.frame:
> as.data.frame.default(DataFrame())
Error in as.data.frame.default(DataFrame()) :
cannot coerce class "structure("DataFrame", package = "IRanges")"
to a data.frame
I think this would work if you defined an S3 as.data.frame method
for DataFrame, instead of an S4 "coerce" method from DataFrame to
data.frame. Try to define the following:
as.data.frame.DataFrame <- selectMethod("as.data.frame", "DataFrame")
A couple of months ago I've started to add some S3 methods to the
IRanges/GenomicRanges infrastructure. So far I only did it for
duplicated, unique, sort, levels, as.list, window, window<-. but
many are still missing (30-40 or more). as.data.frame.DataFrame is
one of them.
Cheers,
H.
## ok fine whatever, I'll do the coercion myself
mat <- model.matrix(~ age + race + sex,
data=as(colData(sortedBrainCells),'data.frame'))
head(mat)
## (Intercept) age raceAsian raceCaucasian sexMale
## 5175-G 1 47 0 1 1
## 5175-N 1 47 0 1 1
## 813-N 1 30 0 1 0
## 1740-N 1 13 0 0 0
## 1546-N 1 14 0 0 0
## 1546-G 1 14 0 0 0
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
