newFlowframe: takes a flowframe, a group indicator and formulates another...

In fomotis/cyanoFilter: Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

Description

takes a flowframe, a group indicator and formulates another flowframe with group indicator as part of the expression matrix of the new flowframe.

Usage

newFlowframe(flowfile, group = NULL, togate = NULL)

Arguments

flowfile	flowframe after debris are removed.
group	cluster group to be added to the expression matrix
togate	channel detected to have more than one peak

Value

flowframe with indicators for particle cluster

Examples

flowfile_path <- system.file("extdata", "B4_18_1.fcs", 
                  package = "cyanoFilter",
              mustWork = TRUE)
flowfile <- flowCore::read.FCS(flowfile_path, alter.names = TRUE,
                               transformation = FALSE, emptyValue = FALSE,
                               dataset = 1) 
flowfile_nona <- cyanoFilter::noNA(x = flowfile)
flowfile_noneg <- cyanoFilter::noNeg(x = flowfile_nona)
flowfile_logtrans <- cyanoFilter::lnTrans(x = flowfile_noneg, 
c('SSC.W', 'TIME'))
oneDgate(flowfile, 'RED.B.HLin')

fomotis/cyanoFilter documentation built on Aug. 1, 2021, 10:58 p.m.