Cyanobacteria Population Identification for Flow Cytometry


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Documentation for package ‘cyanoFilter’ version 0.1.3

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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.