Nothing
R/split-methods.R
In flowCore: flowCore: Basic structures for flow cytometry data
Defines functions
compatibleFilters
## ==========================================================================
## The splitting operation in the context of 'flowFrames' and 'flowSets' is
## the logical extension of subsetting. While the latter only returns
## the events contained within a gate, the former splits the data into
## the groups of events contained within and those not contained within a
## particular gate. This concept is extremely useful in applications where
## gates describe the distinction between positivity and negativity for a
## particular marker.
## Splitting has a special meaning for gates that result in
## 'multipleFilterResults', in which case simple subsetting doesn't make
## much sense (there are multiple populations that are defined by the gate
## and it is not clear which of those should be used for the subsetting
## operation). Accordingly, splitting of multipleFilterResults creates
## multiple subsets. The argument 'population' can be used to limit the
## output to only one or some of the resulting subsets. It takes as values
## a character vector of names of the populations of interest. See the
## documentation of the different filter classes on how population names
## can be defined and the respective default values. For splitting of
## 'logicalFilterResults', the 'population' argument can be used to set
## the population names since there is not reasonable default other than the
## name of the gate. The content of the argument 'prefix' will be prepended
## to the population names and '+' or '-' are finally appended allowing for
## more flexible naming schemes.
## Further control of the output is provided by the argument 'flowSet',
## which defines whether individual subsets should be returned in the form
## of a list (the default) or whether they should be coerced into objects
## of class 'flowSet'. This only applies when splitting 'flowFrames',
## splitting of 'flowSets' always results in lists of 'flowSet' objects.
## ==========================================================================
#' Methods to split flowFrames and flowSets according to filters
#'
#'
#' Divide a flow cytometry data set into several subset according to the
#' results of a filtering operation. There are also methods available to split
#' according to a factor variable.
#'
#'
#' The splitting operation in the context of \code{\linkS4class{flowFrame}}s
#' and \code{\linkS4class{flowSet}}s is the logical extension of subsetting.
#' While the latter only returns the events contained within a gate, the former
#' splits the data into the groups of events contained within and those not
#' contained within a particular gate. This concept is extremely useful in
#' applications where gates describe the distinction between positivity and
#' negativity for a particular marker.
#'
#' The flow data structures in \code{flowCore} can be split into subsets on
#' various levels:
#'
#' \code{\linkS4class{flowFrame}}: row-wise splitting of the raw data. In most
#' cases, this will be done according to the outcome of a filtering operation,
#' either using a filter that identifiers more than one sub-population or by a
#' logical filter, in which case the data is split into two populations: "in
#' the filter" and "not in the filter". In addition, the data can be split
#' according to a factor (or a numeric or character vector that can be coerced
#' into a factor).
#'
#' \code{\linkS4class{flowSet}}: can be either split into subsets of
#' \code{\linkS4class{flowFrame}}s according to a factor or a vector that can
#' be coerced into a factor, or each individual \code{\linkS4class{flowFrame}}
#' into subpopulations based on the \code{\linkS4class{filter}}s or
#' \code{\linkS4class{filterResult}}s provided as a list of equal length.
#'
#' Splitting has a special meaning for filters that result in
#' \code{\linkS4class{multipleFilterResult}}s or
#' \code{\linkS4class{manyFilterResult}}s, in which case simple subsetting
#' doesn't make much sense (there are multiple populations that are defined by
#' the gate and it is not clear which of those should be used for the
#' subsetting operation). Accordingly, splitting of multipleFilterResults
#' creates multiple subsets. The argument \code{population} can be used to
#' limit the output to only one or some of the resulting subsets. It takes as
#' values a character vector of names of the populations of interest. See the
#' documentation of the different filter classes on how population names can be
#' defined and the respective default values. For splitting of
#' \code{\linkS4class{logicalFilterResult}}s, the \code{population} argument
#' can be used to set the population names since there is no reasonable default
#' other than the name of the gate. The content of the argument \code{prefix}
#' will be prepended to the population names and '+' or '-' are finally
#' appended allowing for more flexible naming schemes.
#'
#' The default return value for any of the \code{split} methods is a list, but
#' the optional logical argument \code{flowSet} can be used to return a
#' \code{\linkS4class{flowSet}} instead. This only applies when splitting
#' \code{\linkS4class{flowFrame}}s, splitting of \code{\linkS4class{flowSet}}s
#' always results in lists of \code{\linkS4class{flowSet}} objects.
#'
#' @name split-methods
#' @aliases split-methods split split,flowFrame,ANY-method
#' split,flowFrame,factor-method split,flowFrame,character-method
#' split,flowFrame,numeric-method split,flowFrame,filter-method
#' split,flowFrame,logicalFilterResult-method
#' split,flowFrame,manyFilterResult-method
#' split,flowFrame,multipleFilterResult-method split,flowSet,ANY-method
#' split,flowSet,character-method split,flowSet,factor-method
#' split,flowSet,list-method split,flowSet,numeric-method
#' split,flowSet,filter-method split,flowSet,filterResult-method
#' @docType methods
#' @usage NULL
#' @section Methods:
#'
#' \code{\link{flowFrame}} methods:
#'
#' \describe{
#'
#' \item{split(x = "flowFrame", f = "ANY", drop = "ANY")}{ Catch all input and cast an
#' error if there is no method for \code{f} to dispatch to. }
#'
#' \item{split(x = "flowFrame", f = "factor", drop = "ANY")}{ Split a
#' \code{\link{flowFrame}} by a factor variable. Length of \code{f} should be
#' the same as \code{nrow(x)}, otherwise it will be recycled, possibly leading
#' to undesired outcomes. The optional argument \code{drop} works in the usual
#' way, in that it removes empty levels from the factor before splitting.}
#'
#' \item{split(x = "flowFrame", f = "character", drop = "ANY")}{ Coerce \code{f} to a
#' factor and split on that. }
#'
#' \item{split(x = "flowFrame", f = "numeric", drop = "ANY")}{ Coerce \code{f} to a
#' factor and split on that. }
#'
#' \item{split(x = "flowFrame", f = "filter", drop = "ANY")}{ First applies the
#' \code{\linkS4class{filter}} to the \code{\linkS4class{flowFrame}} and then
#' splits on the resulting \code{\linkS4class{filterResult}} object. }
#'
#' \item{split(x = "flowFrame", f = "logicalFilterResult", drop = "ANY")}{ Split into
#' the two subpopulations (in and out of the gate). The optional argument
#' \code{population} can be used to control the names of the results. }
#'
#' \item{split(x = "flowFrame", f = "manyFilterResult", drop = "ANY")}{ Split into the
#' several subpopulations identified by the filtering operation. Instead of
#' returning a list, the additional logical argument codeflowSet makes the
#' method return an object of class \code{\linkS4class{flowSet}}. The optional
#' \code{population} argument takes a character vector indicating the
#' subpopulations to use for splitting (as identified by the population name in
#' the \code{filterDetails} slot).}
#'
#' \item{split(x = "flowFrame", f = "multipleFilterResult", drop = "ANY")}{ Split into
#' the several subpopulations identified by the filtering operation. Instead of
#' returning a list, the additional logical argument codeflowSet makes the
#' method return an object of class \code{\linkS4class{flowSet}}. The optional
#' \code{population} argument takes a character vector indicating the
#' subpopulations to use for splitting (as identified by the population name in
#' the \code{filterDetails} slot). Alternatively, this can be a list of
#' characters, in which case the populations for each list item are collapsed
#' into one \code{\linkS4class{flowFrame}}.}
#'
#' }
#'
#' \code{\linkS4class{flowSet}} methods:
#'
#' \describe{
#'
#' \item{split(x = "flowSet", f = "ANY", drop = "ANY")}{ Catch all input and cast an
#' error if there is no method for \code{f} to dispatch to. }
#'
#' \item{split(x = "flowSet", f = "factor", drop = "ANY")}{ Split a
#' \code{\link{flowSet}} by a factor variable. Length of \code{f} needs to be
#' the same as \code{length(x)}. The optional argument \code{drop} works in the
#' usual way, in that it removes empty levels from the factor before splitting.
#' }
#'
#' \item{split(x = "flowSet", f = "character", drop = "ANY")}{ Coerce \code{f} to a
#' factor and split on that. }
#'
#' \item{split(x = "flowSet", f = "numeric", drop = "ANY")}{ Coerce \code{f} to a
#' factor and split on that. }
#'
#' \item{split(x = "flowSet", f = "list", drop = "ANY")}{ Split a
#' \code{\link{flowSet}} by a list of \code{\linkS4class{filterResult}}s (as
#' typically returned by filtering operations on a
#' \code{\linkS4class{flowSet}}). The length of the list has to be equal to the
#' length of the \code{\linkS4class{flowSet}} and every list item needs to be a
#' \code{\linkS4class{filterResult}} of equal class with the same parameters.
#' Instead of returning a list, the additional logical argument codeflowSet
#' makes the method return an object of class \code{\linkS4class{flowSet}}. The
#' optional \code{population} argument takes a character vector indicating the
#' subpopulations to use for splitting (as identified by the population name in
#' the \code{filterDetails} slot). Alternatively, this can be a list of
#' characters, in which case the populations for each list item are collapsed
#' into one \code{\linkS4class{flowFrame}}. Note that using the
#' \code{population} argument implies common population names for
#' all\code{\linkS4class{filterResult}}s in the list and there will be an error
#' if this is not the case. }
#'
#' }
#' @author F Hahne, B. Ellis, N. Le Meur
#' @keywords methods
#' @examples
#'
#' data(GvHD)
#' qGate <- quadGate(filterId="qg", "FSC-H"=200, "SSC-H"=400)
#'
#' ## split a flowFrame by a filter that creates
#' ## a multipleFilterResult
#' samp <- GvHD[[1]]
#' fres <- filter(samp, qGate)
#' split(samp, qGate)
#'
#' ## return a flowSet rather than a list
#' split(samp, fres, flowSet=TRUE)
#'
#' ## only keep one population
#' names(fres)
#' ##split(samp, fres, population="FSC-Height+SSC-Height+")
#'
#'
#' ## split the whole set, only keep two populations
#' ##split(GvHD, qGate, population=c("FSC-Height+SSC-Height+",
#' ##"FSC-Height-SSC-Height+"))
#'
#' ## now split the flowSet according to a factor
#' split(GvHD, pData(GvHD)$Patient)
#'
#' @export
## ==========================================================================
## split methods for flowFrame
## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## We actually split on filterResults and multipleFilterResults, so filters
## have to be evaluated first. Note that the 'drop' argument is silently
## ignored when splitting by filter since it doesn't have a clear meaning in
## this application. It does have the expected behaviour when splitting by
## factors, though.
## Evaluate the filter first and split on the filterResult
setMethod("split",
signature=signature(x="flowFrame",
f="filter"),
definition=function(x, f, drop=FALSE, ...)
split(x, filter(x, f), drop=drop, ...))
## Split on logicalFilterResults. This will divide the data set into those
## events that are contained within the gate and those that are not.
#' @export
setMethod("split",
signature=signature(x="flowFrame",
f="logicalFilterResult"),
definition=function(x, f, drop=FALSE, population=NULL, prefix=NULL,
flowSet=FALSE, ...)
{
## take filterID as default population name and prepend prefix
## if necessary
if(is.null(population))
population <- paste(f@filterId, c("+","-"), sep="")
population <- unlist(population)
if(!is.character(population))
stop("'population' must be character scalar.", call.=FALSE)
if(length(population)>2)
stop("Population argument when splitting on logicalFilterResults",
" must be of length 2", call.=FALSE)
allThere <- population %in% names(f)
if(!all(allThere))
stop("The following are not valid population names in this ",
"filterResult:\n\t", paste(population[!allThere],
collapse="\n\t"), call.=FALSE)
if(!is.null(prefix)){
if(!is.character(prefix))
stop("'prefix' must be character vector.", call.=FALSE)
population <- paste(prefix[1:(min(2, length(prefix)))],
population, sep="")
}
out <- structure(list(x[f@subSet, ], x[!f@subSet, ]),
names=names(f))
keyword(out[[1]])$GUID <-
sprintf("%s (%s)", identifier(out[[1]]), names(f)[1])
keyword(out[[2]])$GUID <-
sprintf("%s (%s)", identifier(out[[2]]), names(f)[2])
keep <- match(population, names(f))
out <- out[keep]
if(flowSet){
out <- flowSet(out)
phenoData(out)$population <- population
sampleNames(out) <- population
varMetadata(out)["population", "labelDescription"] <-
"population identifier produced by splitting"
}
return(out)
})
## Split on multipleFilterResults. The argument 'population' can be used to
## select only certain subpopulations
#' @export
setMethod("split",
signature=signature(x="flowFrame",
f="multipleFilterResult"),
definition=function(x, f, drop=FALSE, prefix=NULL, flowSet=FALSE,
population=NULL, ...)
{
if(is.null(population))
population <- names(f)
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
}
pop <- unique(unlist(population))
allThere <- pop %in% names(f)
if(!all(allThere))
stop("The following are not valid population names in this ",
"filterResult:\n\t", paste(pop[!allThere],
collapse="\n\t"), call.=FALSE)
np <- length(population)
if(is.null(prefix))
nn <- names(population)
else{
if(!is.character(prefix))
stop("'prefix' must be character vector.", call.=FALSE)
prefix <- rep(prefix, np)
nn <- paste(prefix[1:np], names(population), sep="")
}
out <- vector(np, mode="list")
names(out) <- nn
i <- 1
for(p in population){
tmp <- lapply(p, function(i) x[f[[i]], ])
combined <- as(as(tmp, "flowSet"), "flowFrame")
cn <- match("Original", colnames(combined))
if(!is.na(cn))
combined <- combined[,-cn]
keyword(combined)$GUID <-
sprintf("%s (%s)", identifier(tmp[[1]]),
paste(p, collapse=","))
out[[i]] <- combined
i <- i+1
}
if(flowSet){
out <- flowSet(out)
phenoData(out)$population <- names(population)
sampleNames(out) <- names(population)
varMetadata(out)["population", "labelDescription"] <-
"population identifier produced by splitting"
}
return(out)
})
## Split on manyFilterResults. FIXME: Need to take a closer look at this
#' @export
setMethod("split",
signature=signature(x="flowFrame",
f="manyFilterResult"),
definition=function(x, f, drop=FALSE, prefix=NULL,
flowSet=FALSE, population=NULL, ...)
{
m <- getMethod("split", signature=signature(x="flowFrame",
f="multipleFilterResult"))
m(x=x, f=f, drop=drop, prefix=prefix, flowSet=flowSet,
population=population, ...)
})
## Split on a factor, or on a vector that is easily coerced into a factor.
## This is just for completeness.
#' @export
setMethod("split",
signature = signature(x = "flowFrame",
f = "factor"),
definition = function(x,
f,
drop = FALSE,
prefix = NULL,
flowSet = FALSE,
...
)
{
if (drop)
f <- factor(f)
nn <- levels(f)
out <- structure(lapply(nn,
function(i) x[f == i,]),
names = if(is.null(prefix)) nn else
paste(prefix, nn, sep = ""))
if(flowSet) {
print(data.frame(name=nn, split=seq_along(nn), row.names=nn))
flowSet(out,phenoData=new("AnnotatedDataFrame",
data=data.frame(name=I(nn), split=seq_along(nn),
row.names=nn),
varMetadata=data.frame(labelDescription=I(c("Name",
"Split")),
row.names=c("name","split"))))
} else out
})
#' @export
setMethod("split",
signature=signature(x="flowFrame",
f="numeric"),
definition=function(x, f, drop=FALSE, prefix=NULL,
flowSet=FALSE, ...)
split(x, factor(f)))
#' @export
setMethod("split",
signature=signature(x="flowFrame",
f="character"),
definition=function(x, f, drop=FALSE, prefix=NULL,
flowSet=FALSE, ...)
split(x, factor(f)))
## Everything else should stop with an error
#' @export
setMethod("split",
signature=signature(x="flowFrame", f="ANY"),
definition=function(x, f, drop=FALSE, prefix=NULL,...)
stop("Don't know how to split a 'flowFrame' by an object of class '",
class(f), "'.", call.=FALSE))
## ==========================================================================
## split methods for flowSet
## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## By default, we try to split the flowSet by using fsApply. As a special
## case, we need to be able to split according to a list of filtes or
## filterResults, but we also need to make sure that this list is valid, i.e.,
## only contains filters or filterResults of the same class, using the same
## parameters, etc.
## Splitting a flowSet always returns a list of flowSets.
## FIXME: How do we treat the cases in which multipleFilterResult produce
## different numbers of populations? We can't collapse to a flowSet any more,
## do we want lists of lists? Or should this be disallowed completely?
## Try and split a flowSet by whatever comes your way...
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="ANY"),
definition=function(x, f, drop=FALSE, population=NULL,
prefix=NULL, ...)
{
## Split always returns a list
sample.name <- sampleNames(x)
fsApply(x,function(y) {
l <- split(y, f, drop, population, prefix, ...)
names(l) <- paste(names(l), "in", sample.name[1])
sample.name <<- sample.name[-1]
l
}, simplify=FALSE)
})
## Split a flowSet by a single filter, by first creating a list of
## filterResult and then working our way through that in the next
## method.
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="filter"),
definition=function(x, f, drop=FALSE, population=NULL,
prefix=NULL, ...)
{
fres <- filter(x,f)
split(x, fres, population=population, prefix=prefix,
...)
})
## Check if two filters are compatible, i.e. are they of the same class,
## do they share the same parameters...
compatibleFilters <- function(f1, f2)
{
if(class(f1) != class(f2))
stop("Classes of filters don't match:\n", class(f1), " vs. ",
class(f2), call.=FALSE)
if(is(f1, "filterResult")){
ff1 <- f1@filterDetails[[1]]$filter
ff2 <- f2@filterDetails[[1]]$filter
if(class(ff1) != class(ff2))
stop("Classes of filters don't match:\n", class(ff1), " vs. ",
class(ff2), call.=FALSE)
if(!(all(parameters(ff1) == parameters(ff2))))
stop("Filter parameters don't match:\n",
paste(parameters(ff1), collapse=", "), " vs. ",
paste(parameters(ff2), collapse=", "), call.=FALSE)
}
}
## Split a flowSet according to a list of filters or filterResults
## of equal length, We make sure that this list makes sense.
## FIXME: Eventually, this function should be deprecated since we represent
## filterResult for a flowSet in filterResultLists now.
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="list"),
function(x, f, drop=FALSE, population=NULL,
prefix=NULL, ...)
{
## A lot of sanity checking up front
sample.name <- sampleNames(x)
lf <- length(f)
lx <- length(x)
if(lf!=lx)
stop("list of filterResults or filters must be same ",
"length as flowSet.", call.=FALSE)
if(!all(sapply(f, is, "filter")))
stop("Second argument must be list of filterResults or filters,",
call.=FALSE)
lapply(f, compatibleFilters, f[[1]])
## split everything or just some populations
## (if multipleFilterResult)
if(is.null(population)){
if(!is.null(names(f[[1]])))
population <- names(f[[1]])
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
}
## FIXME: Do we want to allow for different names when splitting
## flowSets by multipleFilterResults?
if(lf>1 && !identical(unique(as.vector(sapply(f, names))),
names(f[[1]]))){
for(i in 2:lf)
names(f[[i]]) <- names(f[[1]])
warning("Filtering operation produced non-unique population ",
"names.\n Using names of the first frame now.\n",
" Please check parameter descriptions in the ",
"parameter slots\n of the individual flowFrames.",
call.=FALSE)
}
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 <- split(x[[i]], f[[i]], population=tp,
prefix=prefix, flowSet=FALSE, ...)
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"
}
return(finalRes)
})
## FIXME: This should replace the above list method completely at some point
## NOTE: This method now replaces the one with signature("flowSet","list") [Greg Finak <gfinak@fhcrc.org>, 04/13/2011]
#' @export
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@frameId
#f <- f@.Data
#names(f) <- n
#split(x, f, drop=drop, population=NULL, prefix=NULL, ...)
return(finalRes);
})
## Split by frames of flowSet according to a factor, character or numeric.
## Those have to be of the same length as the flowSet. We can't allow for
## drop=TRUE, because this would create invalid sets.
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="factor"),
definition=function(x, f, drop=FALSE, ...)
{
if(!is.atomic(f) || length(f)!=length(x))
stop("split factor must be same length as flowSet",
call.=FALSE)
gind <- split(1:length(f), f, drop=TRUE)
res <- vector(mode="list", length=length(gind))
for(g in seq_along(gind)){
res[[g]] <- x[gind[[g]]]
phenoData(res[[g]])$split <- levels(f)[g]
varMetadata(res[[g]])["split", "labelDescription"] <-
"Split"
}
names(res) <- names(gind)
return(res)
})
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="numeric"),
definition=function(x, f, drop=FALSE, ...)
split(x, factor(f)))
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="character"),
definition=function(x, f, drop=FALSE, ...)
split(x, factor(f)))
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="filterResult"),
definition=function(x, f, drop=FALSE, ...)
stop("Can't split a flowSet by a single filterResult.\n",
"Either provide list of filterResults or a single filter.",
call.=FALSE))
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Defines functions compatibleFilters
## ==========================================================================
## The splitting operation in the context of 'flowFrames' and 'flowSets' is
## the logical extension of subsetting. While the latter only returns
## the events contained within a gate, the former splits the data into
## the groups of events contained within and those not contained within a
## particular gate. This concept is extremely useful in applications where
## gates describe the distinction between positivity and negativity for a
## particular marker.
## Splitting has a special meaning for gates that result in
## 'multipleFilterResults', in which case simple subsetting doesn't make
## much sense (there are multiple populations that are defined by the gate
## and it is not clear which of those should be used for the subsetting
## operation). Accordingly, splitting of multipleFilterResults creates
## multiple subsets. The argument 'population' can be used to limit the
## output to only one or some of the resulting subsets. It takes as values
## a character vector of names of the populations of interest. See the
## documentation of the different filter classes on how population names
## can be defined and the respective default values. For splitting of
## 'logicalFilterResults', the 'population' argument can be used to set
## the population names since there is not reasonable default other than the
## name of the gate. The content of the argument 'prefix' will be prepended
## to the population names and '+' or '-' are finally appended allowing for
## more flexible naming schemes.
## Further control of the output is provided by the argument 'flowSet',
## which defines whether individual subsets should be returned in the form
## of a list (the default) or whether they should be coerced into objects
## of class 'flowSet'. This only applies when splitting 'flowFrames',
## splitting of 'flowSets' always results in lists of 'flowSet' objects.
## ==========================================================================
#' Methods to split flowFrames and flowSets according to filters
#'
#'
#' Divide a flow cytometry data set into several subset according to the
#' results of a filtering operation. There are also methods available to split
#' according to a factor variable.
#'
#'
#' The splitting operation in the context of \code{\linkS4class{flowFrame}}s
#' and \code{\linkS4class{flowSet}}s is the logical extension of subsetting.
#' While the latter only returns the events contained within a gate, the former
#' splits the data into the groups of events contained within and those not
#' contained within a particular gate. This concept is extremely useful in
#' applications where gates describe the distinction between positivity and
#' negativity for a particular marker.
#'
#' The flow data structures in \code{flowCore} can be split into subsets on
#' various levels:
#'
#' \code{\linkS4class{flowFrame}}: row-wise splitting of the raw data. In most
#' cases, this will be done according to the outcome of a filtering operation,
#' either using a filter that identifiers more than one sub-population or by a
#' logical filter, in which case the data is split into two populations: "in
#' the filter" and "not in the filter". In addition, the data can be split
#' according to a factor (or a numeric or character vector that can be coerced
#' into a factor).
#'
#' \code{\linkS4class{flowSet}}: can be either split into subsets of
#' \code{\linkS4class{flowFrame}}s according to a factor or a vector that can
#' be coerced into a factor, or each individual \code{\linkS4class{flowFrame}}
#' into subpopulations based on the \code{\linkS4class{filter}}s or
#' \code{\linkS4class{filterResult}}s provided as a list of equal length.
#'
#' Splitting has a special meaning for filters that result in
#' \code{\linkS4class{multipleFilterResult}}s or
#' \code{\linkS4class{manyFilterResult}}s, in which case simple subsetting
#' doesn't make much sense (there are multiple populations that are defined by
#' the gate and it is not clear which of those should be used for the
#' subsetting operation). Accordingly, splitting of multipleFilterResults
#' creates multiple subsets. The argument \code{population} can be used to
#' limit the output to only one or some of the resulting subsets. It takes as
#' values a character vector of names of the populations of interest. See the
#' documentation of the different filter classes on how population names can be
#' defined and the respective default values. For splitting of
#' \code{\linkS4class{logicalFilterResult}}s, the \code{population} argument
#' can be used to set the population names since there is no reasonable default
#' other than the name of the gate. The content of the argument \code{prefix}
#' will be prepended to the population names and '+' or '-' are finally
#' appended allowing for more flexible naming schemes.
#'
#' The default return value for any of the \code{split} methods is a list, but
#' the optional logical argument \code{flowSet} can be used to return a
#' \code{\linkS4class{flowSet}} instead. This only applies when splitting
#' \code{\linkS4class{flowFrame}}s, splitting of \code{\linkS4class{flowSet}}s
#' always results in lists of \code{\linkS4class{flowSet}} objects.
#'
#' @name split-methods
#' @aliases split-methods split split,flowFrame,ANY-method
#' split,flowFrame,factor-method split,flowFrame,character-method
#' split,flowFrame,numeric-method split,flowFrame,filter-method
#' split,flowFrame,logicalFilterResult-method
#' split,flowFrame,manyFilterResult-method
#' split,flowFrame,multipleFilterResult-method split,flowSet,ANY-method
#' split,flowSet,character-method split,flowSet,factor-method
#' split,flowSet,list-method split,flowSet,numeric-method
#' split,flowSet,filter-method split,flowSet,filterResult-method
#' @docType methods
#' @usage NULL
#' @section Methods:
#'
#' \code{\link{flowFrame}} methods:
#'
#' \describe{
#'
#' \item{split(x = "flowFrame", f = "ANY", drop = "ANY")}{ Catch all input and cast an
#' error if there is no method for \code{f} to dispatch to. }
#'
#' \item{split(x = "flowFrame", f = "factor", drop = "ANY")}{ Split a
#' \code{\link{flowFrame}} by a factor variable. Length of \code{f} should be
#' the same as \code{nrow(x)}, otherwise it will be recycled, possibly leading
#' to undesired outcomes. The optional argument \code{drop} works in the usual
#' way, in that it removes empty levels from the factor before splitting.}
#'
#' \item{split(x = "flowFrame", f = "character", drop = "ANY")}{ Coerce \code{f} to a
#' factor and split on that. }
#'
#' \item{split(x = "flowFrame", f = "numeric", drop = "ANY")}{ Coerce \code{f} to a
#' factor and split on that. }
#'
#' \item{split(x = "flowFrame", f = "filter", drop = "ANY")}{ First applies the
#' \code{\linkS4class{filter}} to the \code{\linkS4class{flowFrame}} and then
#' splits on the resulting \code{\linkS4class{filterResult}} object. }
#'
#' \item{split(x = "flowFrame", f = "logicalFilterResult", drop = "ANY")}{ Split into
#' the two subpopulations (in and out of the gate). The optional argument
#' \code{population} can be used to control the names of the results. }
#'
#' \item{split(x = "flowFrame", f = "manyFilterResult", drop = "ANY")}{ Split into the
#' several subpopulations identified by the filtering operation. Instead of
#' returning a list, the additional logical argument codeflowSet makes the
#' method return an object of class \code{\linkS4class{flowSet}}. The optional
#' \code{population} argument takes a character vector indicating the
#' subpopulations to use for splitting (as identified by the population name in
#' the \code{filterDetails} slot).}
#'
#' \item{split(x = "flowFrame", f = "multipleFilterResult", drop = "ANY")}{ Split into
#' the several subpopulations identified by the filtering operation. Instead of
#' returning a list, the additional logical argument codeflowSet makes the
#' method return an object of class \code{\linkS4class{flowSet}}. The optional
#' \code{population} argument takes a character vector indicating the
#' subpopulations to use for splitting (as identified by the population name in
#' the \code{filterDetails} slot). Alternatively, this can be a list of
#' characters, in which case the populations for each list item are collapsed
#' into one \code{\linkS4class{flowFrame}}.}
#'
#' }
#'
#' \code{\linkS4class{flowSet}} methods:
#'
#' \describe{
#'
#' \item{split(x = "flowSet", f = "ANY", drop = "ANY")}{ Catch all input and cast an
#' error if there is no method for \code{f} to dispatch to. }
#'
#' \item{split(x = "flowSet", f = "factor", drop = "ANY")}{ Split a
#' \code{\link{flowSet}} by a factor variable. Length of \code{f} needs to be
#' the same as \code{length(x)}. The optional argument \code{drop} works in the
#' usual way, in that it removes empty levels from the factor before splitting.
#' }
#'
#' \item{split(x = "flowSet", f = "character", drop = "ANY")}{ Coerce \code{f} to a
#' factor and split on that. }
#'
#' \item{split(x = "flowSet", f = "numeric", drop = "ANY")}{ Coerce \code{f} to a
#' factor and split on that. }
#'
#' \item{split(x = "flowSet", f = "list", drop = "ANY")}{ Split a
#' \code{\link{flowSet}} by a list of \code{\linkS4class{filterResult}}s (as
#' typically returned by filtering operations on a
#' \code{\linkS4class{flowSet}}). The length of the list has to be equal to the
#' length of the \code{\linkS4class{flowSet}} and every list item needs to be a
#' \code{\linkS4class{filterResult}} of equal class with the same parameters.
#' Instead of returning a list, the additional logical argument codeflowSet
#' makes the method return an object of class \code{\linkS4class{flowSet}}. The
#' optional \code{population} argument takes a character vector indicating the
#' subpopulations to use for splitting (as identified by the population name in
#' the \code{filterDetails} slot). Alternatively, this can be a list of
#' characters, in which case the populations for each list item are collapsed
#' into one \code{\linkS4class{flowFrame}}. Note that using the
#' \code{population} argument implies common population names for
#' all\code{\linkS4class{filterResult}}s in the list and there will be an error
#' if this is not the case. }
#'
#' }
#' @author F Hahne, B. Ellis, N. Le Meur
#' @keywords methods
#' @examples
#'
#' data(GvHD)
#' qGate <- quadGate(filterId="qg", "FSC-H"=200, "SSC-H"=400)
#'
#' ## split a flowFrame by a filter that creates
#' ## a multipleFilterResult
#' samp <- GvHD[[1]]
#' fres <- filter(samp, qGate)
#' split(samp, qGate)
#'
#' ## return a flowSet rather than a list
#' split(samp, fres, flowSet=TRUE)
#'
#' ## only keep one population
#' names(fres)
#' ##split(samp, fres, population="FSC-Height+SSC-Height+")
#'
#'
#' ## split the whole set, only keep two populations
#' ##split(GvHD, qGate, population=c("FSC-Height+SSC-Height+",
#' ##"FSC-Height-SSC-Height+"))
#'
#' ## now split the flowSet according to a factor
#' split(GvHD, pData(GvHD)$Patient)
#'
#' @export
## ==========================================================================
## split methods for flowFrame
## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## We actually split on filterResults and multipleFilterResults, so filters
## have to be evaluated first. Note that the 'drop' argument is silently
## ignored when splitting by filter since it doesn't have a clear meaning in
## this application. It does have the expected behaviour when splitting by
## factors, though.
## Evaluate the filter first and split on the filterResult
setMethod("split",
signature=signature(x="flowFrame",
f="filter"),
definition=function(x, f, drop=FALSE, ...)
split(x, filter(x, f), drop=drop, ...))
## Split on logicalFilterResults. This will divide the data set into those
## events that are contained within the gate and those that are not.
#' @export
setMethod("split",
signature=signature(x="flowFrame",
f="logicalFilterResult"),
definition=function(x, f, drop=FALSE, population=NULL, prefix=NULL,
flowSet=FALSE, ...)
{
## take filterID as default population name and prepend prefix
## if necessary
if(is.null(population))
population <- paste(f@filterId, c("+","-"), sep="")
population <- unlist(population)
if(!is.character(population))
stop("'population' must be character scalar.", call.=FALSE)
if(length(population)>2)
stop("Population argument when splitting on logicalFilterResults",
" must be of length 2", call.=FALSE)
allThere <- population %in% names(f)
if(!all(allThere))
stop("The following are not valid population names in this ",
"filterResult:\n\t", paste(population[!allThere],
collapse="\n\t"), call.=FALSE)
if(!is.null(prefix)){
if(!is.character(prefix))
stop("'prefix' must be character vector.", call.=FALSE)
population <- paste(prefix[1:(min(2, length(prefix)))],
population, sep="")
}
out <- structure(list(x[f@subSet, ], x[!f@subSet, ]),
names=names(f))
keyword(out[[1]])$GUID <-
sprintf("%s (%s)", identifier(out[[1]]), names(f)[1])
keyword(out[[2]])$GUID <-
sprintf("%s (%s)", identifier(out[[2]]), names(f)[2])
keep <- match(population, names(f))
out <- out[keep]
if(flowSet){
out <- flowSet(out)
phenoData(out)$population <- population
sampleNames(out) <- population
varMetadata(out)["population", "labelDescription"] <-
"population identifier produced by splitting"
}
return(out)
})
## Split on multipleFilterResults. The argument 'population' can be used to
## select only certain subpopulations
#' @export
setMethod("split",
signature=signature(x="flowFrame",
f="multipleFilterResult"),
definition=function(x, f, drop=FALSE, prefix=NULL, flowSet=FALSE,
population=NULL, ...)
{
if(is.null(population))
population <- names(f)
else if(!all(sapply(population, is, "character")))
stop("'population' must be a single character vector ",
"or a list of character vectors", call.=FALSE)
if(!is.list(population)){
n <- population
population <- as.list(population)
names(population) <- n
}
pop <- unique(unlist(population))
allThere <- pop %in% names(f)
if(!all(allThere))
stop("The following are not valid population names in this ",
"filterResult:\n\t", paste(pop[!allThere],
collapse="\n\t"), call.=FALSE)
np <- length(population)
if(is.null(prefix))
nn <- names(population)
else{
if(!is.character(prefix))
stop("'prefix' must be character vector.", call.=FALSE)
prefix <- rep(prefix, np)
nn <- paste(prefix[1:np], names(population), sep="")
}
out <- vector(np, mode="list")
names(out) <- nn
i <- 1
for(p in population){
tmp <- lapply(p, function(i) x[f[[i]], ])
combined <- as(as(tmp, "flowSet"), "flowFrame")
cn <- match("Original", colnames(combined))
if(!is.na(cn))
combined <- combined[,-cn]
keyword(combined)$GUID <-
sprintf("%s (%s)", identifier(tmp[[1]]),
paste(p, collapse=","))
out[[i]] <- combined
i <- i+1
}
if(flowSet){
out <- flowSet(out)
phenoData(out)$population <- names(population)
sampleNames(out) <- names(population)
varMetadata(out)["population", "labelDescription"] <-
"population identifier produced by splitting"
}
return(out)
})
## Split on manyFilterResults. FIXME: Need to take a closer look at this
#' @export
setMethod("split",
signature=signature(x="flowFrame",
f="manyFilterResult"),
definition=function(x, f, drop=FALSE, prefix=NULL,
flowSet=FALSE, population=NULL, ...)
{
m <- getMethod("split", signature=signature(x="flowFrame",
f="multipleFilterResult"))
m(x=x, f=f, drop=drop, prefix=prefix, flowSet=flowSet,
population=population, ...)
})
## Split on a factor, or on a vector that is easily coerced into a factor.
## This is just for completeness.
#' @export
setMethod("split",
signature = signature(x = "flowFrame",
f = "factor"),
definition = function(x,
f,
drop = FALSE,
prefix = NULL,
flowSet = FALSE,
...
)
{
if (drop)
f <- factor(f)
nn <- levels(f)
out <- structure(lapply(nn,
function(i) x[f == i,]),
names = if(is.null(prefix)) nn else
paste(prefix, nn, sep = ""))
if(flowSet) {
print(data.frame(name=nn, split=seq_along(nn), row.names=nn))
flowSet(out,phenoData=new("AnnotatedDataFrame",
data=data.frame(name=I(nn), split=seq_along(nn),
row.names=nn),
varMetadata=data.frame(labelDescription=I(c("Name",
"Split")),
row.names=c("name","split"))))
} else out
})
#' @export
setMethod("split",
signature=signature(x="flowFrame",
f="numeric"),
definition=function(x, f, drop=FALSE, prefix=NULL,
flowSet=FALSE, ...)
split(x, factor(f)))
#' @export
setMethod("split",
signature=signature(x="flowFrame",
f="character"),
definition=function(x, f, drop=FALSE, prefix=NULL,
flowSet=FALSE, ...)
split(x, factor(f)))
## Everything else should stop with an error
#' @export
setMethod("split",
signature=signature(x="flowFrame", f="ANY"),
definition=function(x, f, drop=FALSE, prefix=NULL,...)
stop("Don't know how to split a 'flowFrame' by an object of class '",
class(f), "'.", call.=FALSE))
## ==========================================================================
## split methods for flowSet
## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## By default, we try to split the flowSet by using fsApply. As a special
## case, we need to be able to split according to a list of filtes or
## filterResults, but we also need to make sure that this list is valid, i.e.,
## only contains filters or filterResults of the same class, using the same
## parameters, etc.
## Splitting a flowSet always returns a list of flowSets.
## FIXME: How do we treat the cases in which multipleFilterResult produce
## different numbers of populations? We can't collapse to a flowSet any more,
## do we want lists of lists? Or should this be disallowed completely?
## Try and split a flowSet by whatever comes your way...
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="ANY"),
definition=function(x, f, drop=FALSE, population=NULL,
prefix=NULL, ...)
{
## Split always returns a list
sample.name <- sampleNames(x)
fsApply(x,function(y) {
l <- split(y, f, drop, population, prefix, ...)
names(l) <- paste(names(l), "in", sample.name[1])
sample.name <<- sample.name[-1]
l
}, simplify=FALSE)
})
## Split a flowSet by a single filter, by first creating a list of
## filterResult and then working our way through that in the next
## method.
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="filter"),
definition=function(x, f, drop=FALSE, population=NULL,
prefix=NULL, ...)
{
fres <- filter(x,f)
split(x, fres, population=population, prefix=prefix,
...)
})
## Check if two filters are compatible, i.e. are they of the same class,
## do they share the same parameters...
compatibleFilters <- function(f1, f2)
{
if(class(f1) != class(f2))
stop("Classes of filters don't match:\n", class(f1), " vs. ",
class(f2), call.=FALSE)
if(is(f1, "filterResult")){
ff1 <- f1@filterDetails[[1]]$filter
ff2 <- f2@filterDetails[[1]]$filter
if(class(ff1) != class(ff2))
stop("Classes of filters don't match:\n", class(ff1), " vs. ",
class(ff2), call.=FALSE)
if(!(all(parameters(ff1) == parameters(ff2))))
stop("Filter parameters don't match:\n",
paste(parameters(ff1), collapse=", "), " vs. ",
paste(parameters(ff2), collapse=", "), call.=FALSE)
}
}
## Split a flowSet according to a list of filters or filterResults
## of equal length, We make sure that this list makes sense.
## FIXME: Eventually, this function should be deprecated since we represent
## filterResult for a flowSet in filterResultLists now.
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="list"),
function(x, f, drop=FALSE, population=NULL,
prefix=NULL, ...)
{
## A lot of sanity checking up front
sample.name <- sampleNames(x)
lf <- length(f)
lx <- length(x)
if(lf!=lx)
stop("list of filterResults or filters must be same ",
"length as flowSet.", call.=FALSE)
if(!all(sapply(f, is, "filter")))
stop("Second argument must be list of filterResults or filters,",
call.=FALSE)
lapply(f, compatibleFilters, f[[1]])
## split everything or just some populations
## (if multipleFilterResult)
if(is.null(population)){
if(!is.null(names(f[[1]])))
population <- names(f[[1]])
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
}
## FIXME: Do we want to allow for different names when splitting
## flowSets by multipleFilterResults?
if(lf>1 && !identical(unique(as.vector(sapply(f, names))),
names(f[[1]]))){
for(i in 2:lf)
names(f[[i]]) <- names(f[[1]])
warning("Filtering operation produced non-unique population ",
"names.\n Using names of the first frame now.\n",
" Please check parameter descriptions in the ",
"parameter slots\n of the individual flowFrames.",
call.=FALSE)
}
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 <- split(x[[i]], f[[i]], population=tp,
prefix=prefix, flowSet=FALSE, ...)
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"
}
return(finalRes)
})
## FIXME: This should replace the above list method completely at some point
## NOTE: This method now replaces the one with signature("flowSet","list") [Greg Finak <gfinak@fhcrc.org>, 04/13/2011]
#' @export
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]])$population <- np
varMetadata(finalRes[[np]])["population", "labelDescription"] <-
"population identifier produced by splitting"
}
#n <- f@frameId
#f <- f@.Data
#names(f) <- n
#split(x, f, drop=drop, population=NULL, prefix=NULL, ...)
return(finalRes);
})
## Split by frames of flowSet according to a factor, character or numeric.
## Those have to be of the same length as the flowSet. We can't allow for
## drop=TRUE, because this would create invalid sets.
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="factor"),
definition=function(x, f, drop=FALSE, ...)
{
if(!is.atomic(f) || length(f)!=length(x))
stop("split factor must be same length as flowSet",
call.=FALSE)
gind <- split(1:length(f), f, drop=TRUE)
res <- vector(mode="list", length=length(gind))
for(g in seq_along(gind)){
res[[g]] <- x[gind[[g]]]
phenoData(res[[g]])$split <- levels(f)[g]
varMetadata(res[[g]])["split", "labelDescription"] <-
"Split"
}
names(res) <- names(gind)
return(res)
})
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="numeric"),
definition=function(x, f, drop=FALSE, ...)
split(x, factor(f)))
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="character"),
definition=function(x, f, drop=FALSE, ...)
split(x, factor(f)))
#' @export
setMethod("split",
signature=signature(x="flowSet",
f="filterResult"),
definition=function(x, f, drop=FALSE, ...)
stop("Can't split a flowSet by a single filterResult.\n",
"Either provide list of filterResults or a single filter.",
call.=FALSE))
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