replace_phedata_ranges: Replace range data in the pData(parameters(ff)) slot

In rogerswt/wadeTools: Wade's Hodgepodge of Flow Cytometry Functions

Replace range data in the pData(parameters(ff)) slot

Description

We found that round-tripping a flowFrame by first write.FCS followed by read.FCS caused weird effects in the phenodata of the resulting flowFrame. This function replaces the screwed up range numbers with ones stored from before the read-back.

Usage

replace_phedata_ranges(ff, range = NULL, minRange = NULL, maxRange = NULL)

Arguments

ff	The flowFrame to be processed
range	The range values to replace those in ff
minRange	The minRange values to replace those in ff
maxRange	The maxRange values to replace those in ff

Details

This function should be used with care. The range values are affected by the per-parameter transformations that may or may not have been previously applied. There is currently no good mechanism to track them.

The default values of NULL for range, minRange and maxRange result in the generation of values appropriate for data that have been (a) linearly scaled to 0-5.4 on scattering parameters, and (b) biexponentially transformed (using biexpTransform) on the fluorescence parameters. Otherwise, care should be taken to supply range, minRange and maxRange vectors having the same length as ncol(ff).

Value

A flowFrame with replace range values.

rogerswt/wadeTools documentation built on Feb. 16, 2023, 7:47 a.m.