Accessor and replacement methods for items in the description slot (usually
read in from a FCS file header). It lists the
keywords and its values
for a flowFrame specified by a character vector. Additional methods for
lists exists for more programmatic access to the
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
flowFrame. This 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
Return values for
all keywords from the
description slot in
object that match
the character vector
Apply the function in
keyword on the
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
flowFrame and combine it with one or several other keywords.
Combine characters and functions in a list to select keyword values.
This is essentially an
description and returns all keyword-value pairs.
This is a wrapper around
fsApply(object, keyword, keyword) which essentially iterates over the
frames in the
This first coerces the
keyword (mostly a character vector) to a list and then calls the next
N LeMeur,F Hahne,B Ellis
1 2 3 4 5 6 7 8 9 10 11 12 13
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)[["foo"]] <- "bar" data(GvHD) keyword(GvHD, list("GUID", cellnumber=function(x) nrow(x)))
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