Methods to retrieve keywords of a flowFrame
Accessor and replacement methods for items in the description slot
(usually read in from a FCS file header). It lists the
and its values for a flowFrame specified by a character
vector. Additional methods for
for more programmatic access to the keywords.
keyword(object, keyword, ...)
Object of class
Character vector or list of potential keywords or function. If missing all keywords are returned.
compact: logical scaler to indicate whether to hide all the cytometer instrument and laser settings from keywords.
keyword methods allow access to the keywords stored in the
FCS files, either for a
flowFrame or for a list of frames in a
flowSet. The most simple use case is to provide a character
vector or a list of character strings of keyword names. A more
sophisticated version is to provide a function which has to take one
mandatory argument, the value of this is the
can be used to query arbitrary information from the
description slot or even the raw data. The function has to
return a single character string. The
list methods allow to
combine functional and direct keyword access.
The replacement method takes a named character vector or a named list
as input. R's usual recycling rules apply when replacing keywords for
- object = "flowFrame", keyword = "character"
Return values for all keywords from the
objectthat match the character vector
- object = "flowFrame", keyword = "function"
Apply the function in
object. The function needs to be able to cope with a single argument and it needs to return a single character string. A typical use case is for instance to paste together values from several different keywords or to compute some statistic on the
flowFrameand combine it with one or several other keywords.
- object = "flowFrame", keyword = "list"
Combine characters and functions in a list to select keyword values.
- object = "flowFrame", keyword = "missing"
This is essentially an alias for
descriptionand returns all keyword-value pairs.
- object = "flowSet", keyword = "list"
This is a wrapper around
fsApply(object, keyword, keyword)which essentially iterates over the frames in the
- object = "flowSet", keyword = "ANY"
This first coerces the
keyword(mostly a character vector) to a list and then calls the next applicable method.
N LeMeur,F Hahne,B Ellis
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samp <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore")) keyword(samp) keyword(samp, compact = TRUE) keyword(samp, "FCSversion") keyword(samp, function(x,...) paste(keyword(x, "SAMPLE ID"), keyword(x, "GUID"), sep="_")) keyword(samp) <- list(foo="bar") data(GvHD) keyword(GvHD, list("GUID", cellnumber=function(x) nrow(x))) keyword(GvHD) <- list(sample=sampleNames(GvHD))