Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

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... |

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