goodfcs: indicates if measurement from a flowfile is good or bad.

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

Description

This function examines the column containig cells/μ L and determins if the measurement can be used for further analysis or not based on a supplied range.

Usage

goodFcs(metafile, col_cpml = "CellspML", mxd_cellpML = 1000, mnd_cellpML = 50)

Arguments

metafile	associated metafile to the supplied fcsfile. This is a csv file containig computed stats from the flow cytometer.
col_cpml	column name or column number in metafile containing cell per microlitre measurements.
mxd_cellpML	maximal accepted cell per microlitre. Flowfiles with larger cell per microlitre are termed bad. Defaults to 1000.
mnd_cellpML	minimum accepted cell per microlitre. Flowfiles with lesser cell per microlitre are termed bad. Defaults to 50.

Details

Most flow cytometer makers will always inform clients within which range can measurements from the machine be trusted. The machines normally stores the amount of cells/μ L it counted in a sample. Too large value could mean possible doublets and too low value could mean too little cells.

Value

character vector with length same as the number of rows in the metafile whose entries are good for good files and bad for bad files.

Examples

require("stringr")
 metadata <- system.file("extdata", "2019-03-25_Rstarted.csv", 
 package = "cyanoFilter",
              mustWork = TRUE)
 metafile <- read.csv(metadata, skip = 7, stringsAsFactors = FALSE,
                     check.names = TRUE, encoding = "UTF-8")
 metafile <- metafile[, seq_len(65)] #first 65 columns contains useful information
 #extract the part of the Sample.ID that corresponds to BS4 or BS5
 metafile$Sample.ID2 <- stringr::str_extract(metafile$Sample.ID, "BS*[4-5]")
 #clean up the Cells.muL column
 names(metafile)[which(stringr::str_detect(names(metafile), 
 "Cells."))] <- "CellspML"
 goodFcs(metafile = metafile, col_cpml = "CellspML", mxd_cellpML = 1000, 
 mnd_cellpML = 50)

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