FCStSNE: tSNE and OneSENSE algorithm for FCS data

In oneSENSE: One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)

Description

tSNE and OneSENSE algorithm for FCS data

Usage

FCStSNE(LoaderPATH = "fcs", ceil = 5000, FNnames = "names.csv",
  OutputSuffix = "Out", DotSNE = TRUE, DoOneSENSE = TRUE, Bins = 250)

Arguments

LoaderPATH	Path where FCS file is located
ceil	Maximum number of cells to sample from each fcs sample/file
FNnames	.csv file generated when markers from each category are selected
OutputSuffix	suffix to name output folder
DotSNE	boolean, if TRUE do tSNE, if FALSE skip tSNE
DoOneSENSE	boolean, if TRUE do OneSENSE, if FALSE skip OneSENSE
Bins	number of bins to put the cell data into, DEFAULT = 250

Value

FCS files, tSNE histograms, OneSENSE plot

Examples

#dir <- system.file('extdata/fcs', package='oneSENSE')
#FCStSNE(LoaderPATH=dir, FNnames=fnnames) #remove hash symbol to run

Example output

Loading required package: webshot
Loading required package: shiny
Loading required package: shinyFiles
Loading required package: scatterplot3d

oneSENSE documentation built on Nov. 8, 2020, 4:58 p.m.