Methods to retrieve keywords of a flowFrame

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Description

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.

Usage

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keyword(object, keyword, ...)

Arguments

object

Object of class flowFrame.

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.

Details

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

Methods

object = "flowFrame", keyword = "character"

Return values for all keywords from the description slot in object that match the character vector keyword.

object = "flowFrame", keyword = "function"

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.

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 description and 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 flowSet.

object = "flowSet", keyword = "ANY"

This first coerces the keyword (mostly a character vector) to a list and then calls the next applicable method.

Author(s)

N LeMeur,F Hahne,B Ellis

See Also

description

Examples

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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))

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