Cyanobacteria Population Identification for Flow Cytometry

Documentation for package ‘cyanoFilter’ version 0.1.3

cyanoFilter-package	cyanoFilter: A package to identify and/or assign indicators to BS4, BS5 cyanobacteria cells contained in water sample.
bs4_nc	gates out or assign indicators to Synechococcus cyanobacteria cells in the bottom right of the 2-D space.
bs5_nc	gates out or assign indicators to Synechococcus cyanobacteria cells in the top right of the 2-D space.
celldebris_emclustering	identifies Synechococcus cyanobacteria cells and Debris in a flowfile using an EM style algorithm.
celldebris_nc	gates out or assign indicators to Synechococcus cyanobacteria cells.
cellmargin	Removes or assign indicators to margin events.
cluster_plot	plots the expression matrix of a flowframe analysed with celldebris_emclustering.
cyanoFilter	cyanoFilter: A package to identify and/or assign indicators to BS4, BS5 cyanobacteria cells contained in water sample.
debris_inc	gates out or assign indicators to debris particle.
debris_nc	gates out or assign indicators to debris particle.
goodfcs	indicates if measurement from a flowfile is good or bad.
lnTrans	log transforms the expression matrix of a flowframe
mvnorm	multivariate normal density
nona	Removes NA values from the expression matrix of a flow cytometer file.
noneg	Removes negative values from the expression matrix
pair_plot	plots the expression matrix of a flowframe. Note that, it takes some time to display the plot.
retain	Decides if a file should be retiained or removed based on its status.