| accTest | tests the accuracy of several automated gating functions on... |
| accuracy | samples two rows in a matrix and check if the samples are... |
| 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... |
| cyanoFilter | cyanoFilter: A package to identify and cluster phytoplankton... |
| DebrisFilter | the Debris class |
| debrisNc | gates out or assign indicators to debris particle based on... |
| fullFlowframe | generic function for extracting the full flowframe |
| fullFlowframe-DebrisFilter-method | accesor method for reduced flowframe (DebrisFilter class) |
| fullFlowframe-MarginEvents-method | accesor method for the fullflowframe (MarginEvent class) |
| fullFlowframe-PhytopFilter-method | accesor method for full flowframe(PhytoFilter class) |
| gateFunc | tests the accuracy of several automated gating functions on... |
| getChannel | returns the channel with more than one peak present. It... |
| ggpairsDens | produces a scatter plot of the expression matrix of the... |
| ggplotDens | plots two channels of a flowframe. |
| ggplotDens2 | plots two channels of a flowframe with different colors for... |
| goodfcs | indicates if measurement from a flowfile is good or bad. |
| is.DebrisFilter | function to check if object is of class... |
| 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... |
| is.PhytopFilter | function to check if object is of class... |
| lnTrans | log transforms the expression matrix of a flowframe |
| MarginEvents | the marginEvent class |
| newFlowframe | takes a flowframe, a group indicator and formulates another... |
| nona | Removes NA values from the expression matrix of a flow... |
| noneg | Removes negative values from the expression matrix |
| oneDgate | returns the labels stating the cluster of each row in a... |
| pairsPlot | produces a scatter plot of the expression matrix of a... |
| PhytoFilter | gates out and assign indicators to phytoplankton cells based... |
| PhytopFilter | the phytofilter class |
| pigmentGate | gates out or assign indicators to phytoplankton cells based... |
| plot-DebrisFilter-ANY-method | plot method for DebrisFilter objects |
| plot-MarginEvents-ANY-method | plot method for MarginEvents objects |
| plot-PhytopFilter-ANY-method | plot method for PhytoFilter objects |
| reducedFlowframe | generic function for extracting the full flowframe |
| reducedFlowframe-DebrisFilter-method | accesor method for reduced flowframe (DebrisFilter class) |
| reducedFlowframe-MarginEvents-method | accesor method for reduced flowframe (MarginEvent class) |
| reducedFlowframe-PhytopFilter-method | accesor method for reduced flowframe(PhytoFilter class) |
| retain | Decides if a file should be retiained or removed based on its... |
| rowNumbers | returns the position of the cells below, above or between... |
| summaries | takes a flowframes, a vector of channels, cluster indicator... |
| summaries-DebrisFilter-method | takes a flowframes, a vector of channels, cluster indicator... |
| summaries-MarginEvents-method | takes a flowframes, a vector of channels, cluster indicator... |
| summaries-PhytopFilter-method | takes a flowframes, a vector of channels, cluster indicator... |
