ncfsApply-ncdfFlowSet-method: apply method for ncdfFlowSet (for internal use)

In RGLab/ncdfFlow: ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.

apply method for ncdfFlowSet (for internal use)

Description

It is equivalent to fsApply. But the latter could cause memory issue when FUN returns a flowFrame. ncfsApply writes to a new cdf file instead of memory. Thus it will return a ncdfFlowSet object.

Usage

## S4 method for signature 'ncdfFlowSet'
ncfsApply(x, FUN, ..., use.exprs = FALSE, ncdfFile = NULL)

Arguments

x	ncdfFlowSet
FUN	function to apply
...	other arguments to pass to FUN
use.exprs	logical see fsApply
ncdfFile	A character scalar giving the output file name. By default, It is NULL and the function will generate a random file name, potentially adding the .cdf suffix unless a file extension is already present.

Details

When the function given by argument "FUN" does not return the entire flowFrame object with the same size of the original one (such as compensate,transform...), fsApply should be used instead.

Examples

data(GvHD)
nc <- ncdfFlowSet(GvHD[1:2])

#use fsApply when FUN does not return a flowFrame 
fsApply(nc, nrow)
fsApply(nc, range)

#use ncfsApply when FUN returns a flowFrame
lgcl <- logicleTransform( w = 0.5, t= 10000, m =4.5)
translist <- transformList(c("FL1-H", "FL2-H"), lgcl)
nc1 <- ncfsApply(nc, transform, translist)

RGLab/ncdfFlow documentation built on July 5, 2022, 10:20 a.m.