Function reference • flowdex

Package flowdex

flowdex: Extract Fluorescence Distribution Data from FCS Files and Recalculate to Events per Volume

Setup Functions

setup_settings(): Perform Settings Setup

genfs(): Generate Folder Structure

fd_update_settings(): Manually Update the Settings

Repair Functions

checkRepairFcsFiles(): Check and Repair FCS Files

repairVolumes(): Repair Volume Values in FCS Files

repairSID(): Repair a Single Sample ID

Gating & Data Extraction

flowdexit(): Read in FCS Files and Extract Data

makefdmat(): Extract Fluorescence Distribution Matrix

makeGatingSet(): Make Gating Set

makeAddGatingSet(): Make Gating Set and Add Gates

addGates(): Add Polygon Gates

getEventsPerVolume(): Get Events per Volume Unit

cutFdmatToGate(): Cut 'fdmat' Object to Gate

exportFdmatData(): Export Fluorescence Distributions

Plot Functions

drawGate(): Manually Draw Polygon Gate

plotgates(): Plot Gates on All flowFrames in a Gating Set

plotFlscDist(): Plot Fluorescence Distribution

Accessory Functions

fd_save(): Save Fluorescence Distribution 'fdmat' Object

fd_load(): Load Fluorescence Distribution 'fdmat' Object

applyBandpass(): Apply Bandpass Filter to Fluorescence Intensities

Class Documentation

class-eventsPV: Class 'eventsPV'

class-cyTags: Class 'cyTags'

class-gatingStrategy_fd: Class 'gatingStrategy_fd'

class-GatingSet_fd: Class 'GatingSet_fd'

class-fdmat_single: Class 'fdmat_single'

class-fdmat: Class 'fdmat'

Other Functions

check_download_data(): Check and Download Example Dataset