lnTrans: log transforms the expression matrix of a flowframe

In cyanoFilter: Cyanobacteria Population Identification for Flow Cytometry

Description

log transforms the expression matrix of a flowframe

Usage

lnTrans(x, notToTransform = c("SSC.W", "TIME"))

Arguments

x	flowframe to be transformed
notToTransform	columns not to be transformed

Value

flowframe with log transformed expression matrix

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) #FCS file contains only one data object
flowfile_nona <- cyanoFilter::nona(x = flowfile)
flowfile_noneg <- cyanoFilter::noneg(x = flowfile_nona)
lnTrans(x = flowfile_noneg, c('SSC.W', 'TIME'))

cyanoFilter documentation built on Jan. 9, 2020, 5:08 p.m.