Hi, Aric
Looking at the source code for split(signature("flowSet","list")) in
flowCore, the function presumes that the number of populations in each
filterResult is equal, which is clearly not the case here. There are
notes in the code that this is a problem, so it seems to be a known
bug.
Below is a modified "split" method for
signature("flowSet","filterResultList").
I'll work on getting this fix into the development version.
setMethod("split",
signature=signature(x="flowSet",
f="filterResultList"),
definition=function(x, f, drop=FALSE, population=NULL,
prefix=NULL, ...)
{
lf<-length(f)
sample.name <- sampleNames(x)
if(length(x)!=length(f)){
stop("filterResultList and flowSet must be
same ",
"length.", call.=FALSE)
}
lapply(f, flowCore:::compatibleFilters, f[[1]])
if(is.null(population)){
if(all(unlist(lapply(f,function(q)!is.null(names(q))))))
population<-unique(unlist(lapply(f,names)))
else
population <- c("positive", "negative")
} else if(!all(sapply(population, is, "character")))
stop("'population' must be a single character vector ",
"or a list of character vectors", call.=FALSE)
if(!is.list(population)){
n <- population
population <- as.list(population)
names(population) <- n
}
finalRes <- vector(mode="list", length=length(population))
names(finalRes) <- names(population)
for(p in seq_along(population)){
tp <- population[p]
res <- vector(mode="list", length=lf)
for(i in 1:lf){
l <- try(split(x[[i]], f[[i]],
population=tp,
prefix=prefix, flowSet=FALSE,
...),silent=TRUE)
if(inherits(l,"try-error")){
if(geterrmessage()==paste("Error : The following are not valid
population names in this filterResult:\n\t",tp,"\n",sep="")){
message("Creating an
empty flowFrame for population ",tp,"\n")
#Create an empty
flowFrame
l<-x[[i]][0,];
identifier(l)<-paste(identifier(l),paste("(",tp,")",sep=""),sep=" ")
l<-list(l);
}else
stop("Can't split
flowFrame ",sampleNames(x[i])," on population ",tp);
}
res[[i]] <- l[[1]]
if(!is.null(prefix)){
if(is.logical(prefix) && prefix)
names(res)[i] <- paste(names(l), "in",
sample.name[i])
else if(is.character(prefix))
names(res)[i] <- paste(prefix, sample.name[i])
}else
names(res)[i] <- sample.name[i]
}
np <- names(population)[p]
finalRes[[np]] <- flowSet(res, phenoData=phenoData(x))
phenoData(finalRes[[np]])$population <- np
varMetadata(finalRes[[np]])["population", "labelDescription"]
<-
"population identifier produced by splitting"
}
#n <- f at frameId
#f <- f at .Data
#names(f) <- n
#split(x, f, drop=drop, population=NULL, prefix=NULL, ...)
return(finalRes);
})
On 2011-04-12, at 5:21 PM, Aric Gregson wrote:
> Hello,
>
> I am attempting to split out flowSet result from a curv2Filter
applied to
> a flowSet. I realize that to split without using the 'population'
> argument all samples must have the same populations, which is not
the
> case here. Plotting the result of the filter shows populations 'area
1'
> through 'area 4'. I am interested in obtaining 'area 3' which is
present
> in flowFrames 1, 2 and 5. I attempt this with the following code:
>
>> nk <- split(Data(wf[['NK-']])[c(1,2,5)], filter_cv2_cd3,
> population="area 3")
> Error in `names<-`(`*tmp*`, value = c("rest", "area 1", "area 2",
"area 3" :
> Length of replacement vector doesn't match.
>
> which suggests to me that it is ignoring the 'population'
> argument. Taking a look at the result 'nk' confirms this:
>
>> nk
> $rest
> A flowSet with 2 experiments....
>
> $`area 1`
> A flowSet with 2 experiments....
>
> $`area 2`
> A flowSet with 2 experiments....
>
> $`area 3`
> A flowSet with 2 experiments....
>
> These flowFrames do not have an 'area 4'. Is this not the proper way
to
> go about splitting the flowSet or is 'split' not functioning
correctly?
>
> Thanks in advance for any suggestions.
>
> Aric
> (flowCore 1.16.0)
>
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Greg Finak, PhD
Post-doctoral Research Associate
PS Statistics, Vaccine and Infectious Disease Division.
Fred Hutchinson Cancer Research Center
Seattle, WA
(206)667-3116
gfinak at fhcrc.org
Greg Finak, PhD
Post-doctoral Research Associate
PS Statistics, Vaccine and Infectious Disease Division.
Fred Hutchinson Cancer Research Center
Seattle, WA
(206)667-3116
gfinak at fhcrc.org
Greg Finak, PhD
Post-doctoral Research Associate
PS Statistics, Vaccine and Infectious Disease Division.
Fred Hutchinson Cancer Research Center
Seattle, WA
(206)667-3116
gfinak at fhcrc.org
