keyword-methods {flowCore} | R Documentation |
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 function
and lists
exists
for more programmatic access to the keywords.
keyword(object, keyword, ...)
object |
Object of class |
keyword |
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. |
The 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 flowFrames
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
a whole flowSet
Return values for
all keywords from the description
slot in object
that match the character vector keyword
.
Apply the function
in keyword
on the flowFrame
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 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
alias for description
and returns all keyword-value
pairs.
This is a wrapper around
fsApply(object, keyword, keyword)
which essentially
iterates over the frames in the flowSet
.
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
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))