Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

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Documentation for package ‘cyanoFilter’ version 1.12.0

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accTest tests the accuracy of several automated gating functions on monoculture flow cytometry experiments.
accuracy samples two rows in a matrix and check if the samples are similar or different based on their cluster labels
cellMargin Removes or assign indicators to margin events.
clusterExtract extract clusters based on supplied cluster indicator
clusterExtractp takes a flowframe, name of cluster column and extracts part of flowframe that makes up proportion.
cyanoFilter cyanoFilter: A package to identify and cluster phytoplankton cells contained in flow cytometry data.
DebrisFilter the Debris class
debrisNc gates out or assign indicators to debris particle based on their chlorophyll expression.
fullFlowframe generic function for extracting the full flowframe
fullFlowframe-method accesor method for reduced flowframe (DebrisFilter class)
fullFlowframe-method accesor method for the fullflowframe (MarginEvent class)
fullFlowframe-method accesor method for full flowframe(PhytoFilter class)
gateFunc tests the accuracy of several automated gating functions on monoculture flow cytometry experiments.
getChannel returns the channel with more than one peak present. It returns NA if there is only one peak present.
ggpairsDens produces a scatter plot of the expression matrix of the flowframe. If a cluster variable is given, it assigns different colors to the clusters.
ggplotDens plots two channels of a flowframe.
ggplotDens2 plots two channels of a flowframe with different colors for clusters identified.
goodFcs indicates if measurement from a flowfile is good or bad.
is.DebrisFilter function to check if object is of class cyanoFilter(DebrisFilter)
is.flowFrame function to check if object is a flowFrame
is.flowSet function to check if object is a flowSet
is.MarginEvents function to check if object is of class cyanoFilter(MarginEvents)
is.PhytopFilter function to check if object is of class cyanoFilter(PhytoFilter)
lnTrans log transforms the expression matrix of a flowframe
MarginEvents the marginEvent class
newFlowframe takes a flowframe, a group indicator and formulates another flowframe with group indicator as part of the expression matrix of the new flowframe.
noNA Removes NA values from the expression matrix of a flow cytometer file.
noNeg Removes negative values from the expression matrix
oneDgate returns the labels stating the cluster of each row in a flowfile.
pairsPlot produces a scatter plot of the expression matrix of a flowframe. Note that, it takes some time to display the plot.
phytoFilter gates out and assign indicators to phytoplankton cells based on the expression of measured cell complexity channels.
PhytopFilter the phytofilter class
pigmentGate gates out or assign indicators to phytoplankton cells based on the expression of the measured pigments.
plot-method plot method for DebrisFilter objects
plot-method plot method for MarginEvents objects
plot-method plot method for PhytoFilter objects
reducedFlowframe generic function for extracting the full flowframe
reducedFlowframe-method accesor method for reduced flowframe (DebrisFilter class)
reducedFlowframe-method accesor method for reduced flowframe (MarginEvent class)
reducedFlowframe-method accesor method for reduced flowframe(PhytoFilter class)
retain Decides if a file should be retiained or removed based on its status.
rowNumbers returns the position of the cells below, above or between estimated gates
summaries takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster
summaries-method takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster
summaries-method takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster
summaries-method takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster