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| 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 reduced flowframe(PhytoFilter class) |
| 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.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 |