immunoClust Cell-clustering Sample

Description

flowFrame data sample with 10.000 events in 7 parameters.

Usage

data(dat.fcs)

Details

This FCS sample is a reduced (10.000 events) dataset in flowFrame format of the first sample in the dataset of immunoClust, MACS-depleted populations datasets 2010. URL http://flowrepository.org/id/FR-FCM-ZZWB.

Value

A flowCore flowFrame with 10.000 observations on the following 7 parameters.

FCS-A

Forward scatter

SSC-A

Sideward scatter

FITC-A

CD14

PE-A

CD19

APC-A

CD15

APC-Cy7-A

CD4

Pacific Blue-A

CD3

Source

http://flowrepository.org/id/FR-FCM-ZZWB

Examples

data(dat.fcs)

## process cell clustering
dat.res <- cell.process(dat.fcs)

## apply asinh-transformation
dat.fcs.transformed <- trans.ApplyToData(dat.res, dat.fcs)

## plot results
splom(dat.res, dat.fcs.transformed)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(immunoClust)
Loading required package: grid
Loading required package: lattice
Loading required package: flowCore
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/immunoClust/dat.fcs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dat.fcs
> ### Title: immunoClust Cell-clustering Sample
> ### Aliases: dat.fcs
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(dat.fcs)
> 
> ## process cell clustering
> dat.res <- cell.process(dat.fcs)
filtered from above:318
filtered from below:0

Test cluster 1 for sub-clustering
EM takes 0.017 mins minutes
cluster 1 has 2 sub-cluster at 2, ICL=149
cluster 1 has 2 sub-cluster at 2, ICL=0
split cluster 1 into 2 sub-cluster
Model Refinement takes 0.017 mins minutes

Fit Model 1 of (6/10) K=1->2 N=302
EM takes 0 mins minutes

Test cluster 1 for sub-clustering
EM takes 0 mins minutes
Test cluster 2 for sub-clustering
EM takes 0.017 mins minutes
cluster 1 has 2 sub-cluster at 2, ICL=133
cluster 2 has 4 sub-cluster at 4, ICL=41
cluster 1 has 2 sub-cluster at 2, ICL=0
split cluster 1 into 2 sub-cluster
split cluster 2 into 4 sub-cluster
Model Refinement takes 0.017 mins minutes

Fit Model 2 of (6/10) K=2->6 N=605
EM takes 0 mins minutes

Test cluster 1 for sub-clustering
EM takes 0 mins minutes
Test cluster 2 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 3 for sub-clustering
EM takes 0 mins minutes
Test cluster 4 for sub-clustering
EM takes 0 mins minutes
Test cluster 5 for sub-clustering
EM takes 0 mins minutes
Test cluster 6 for sub-clustering
EM takes 0 mins minutes
cluster 2 has 2 sub-cluster at 2, ICL=108
cluster 3 has 2 sub-cluster at 2, ICL=21
cluster 6 has 7 sub-cluster at 8, ICL=4
split cluster 2 into 2 sub-cluster
Model Refinement takes 0.017 mins minutes

Fit Model 3 of (6/10) K=6->7 N=1210
EM takes 0 mins minutes

Test cluster 1 for sub-clustering
EM takes 0 mins minutes
Test cluster 2 for sub-clustering
EM takes 0 mins minutes
Test cluster 3 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 4 for sub-clustering
EM takes 0 mins minutes
Test cluster 5 for sub-clustering
EM takes 0 mins minutes
Test cluster 6 for sub-clustering
EM takes 0.017 mins minutes
cluster 4 has 3 sub-cluster at 3, ICL=54
cluster 2 has 2 sub-cluster at 2, ICL=30
cluster 5 has 5 sub-cluster at 6, ICL=15
cluster 3 has 6 sub-cluster at 7, ICL=10
cluster 1 has 3 sub-cluster at 3, ICL=9.7
cluster 1 has 3 sub-cluster at 3, ICL=0
split cluster 4 into 3 sub-cluster
Model Refinement takes 0.033 mins minutes

Fit Model 4 of (6/10) K=6->8 N=2420
EM takes 0 mins minutes

Test cluster 1 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 2 for sub-clustering
EM takes 0 mins minutes
Test cluster 3 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 4 for sub-clustering
EM takes 0 mins minutes
Test cluster 5 for sub-clustering
EM takes 0 mins minutes
Test cluster 6 for sub-clustering
EM takes 0 mins minutes
Test cluster 7 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 8 for sub-clustering
EM takes 0.017 mins minutes
cluster 1 has 2 sub-cluster at 2, ICL=52
cluster 2 has 5 sub-cluster at 6, ICL=20
cluster 7 has 7 sub-cluster at 7, ICL=18
cluster 3 has 8 sub-cluster at 8, ICL=13
cluster 4 has 4 sub-cluster at 6, ICL=11
cluster 5 has 2 sub-cluster at 2, ICL=6.5
cluster 1 has 2 sub-cluster at 2, ICL=0
split cluster 1 into 2 sub-cluster
Model Refinement takes 0.067 mins minutes

Fit Model 5 of (6/10) K=8->9 N=4841
EM takes 0.017 mins minutes

Test cluster 1 for sub-clustering
EM takes 0 mins minutes
Test cluster 2 for sub-clustering
EM takes 0 mins minutes
Test cluster 3 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 4 for sub-clustering
EM takes 0 mins minutes
Test cluster 5 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 6 for sub-clustering
EM takes 0 mins minutes
Test cluster 7 for sub-clustering
EM takes 0 mins minutes
Test cluster 8 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 9 for sub-clustering
EM takes 0.033 mins minutes
cluster 8 has 4 sub-cluster at 4, ICL=33
cluster 6 has 4 sub-cluster at 4, ICL=26
cluster 3 has 2 sub-cluster at 2, ICL=24
cluster 5 has 5 sub-cluster at 6, ICL=13
cluster 1 has 3 sub-cluster at 3, ICL=11
cluster 4 has 2 sub-cluster at 2, ICL=8.8
cluster 1 has 3 sub-cluster at 3, ICL=0
Model Refinement takes 0.083 mins minutes

Fit Model 6 of (6/10) K=9->9 N=9682
EM takes 0 mins minutes

Test cluster 1 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 2 for sub-clustering
EM takes 0 mins minutes
Test cluster 3 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 4 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 5 for sub-clustering
EM takes 0 mins minutes
Test cluster 6 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 7 for sub-clustering
EM takes 0 mins minutes
Test cluster 8 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 9 for sub-clustering
EM takes 0.033 mins minutes
cluster 8 has 3 sub-cluster at 3, ICL=65
cluster 4 has 2 sub-cluster at 2, ICL=51
cluster 6 has 4 sub-cluster at 4, ICL=43
cluster 3 has 3 sub-cluster at 3, ICL=38
cluster 2 has 2 sub-cluster at 2, ICL=30
cluster 1 has 3 sub-cluster at 3, ICL=29
cluster 5 has 5 sub-cluster at 6, ICL=6.5
cluster 7 has 3 sub-cluster at 4, ICL=6.3
cluster 1 has 3 sub-cluster at 3, ICL=0
split cluster 4 into 2 sub-cluster
split cluster 8 into 3 sub-cluster
Model Refinement takes 0.12 mins minutes

Fit Model 7 of (6/10) K=9->12 N=9682
EM takes 0 mins minutes

Test cluster 1 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 2 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 3 for sub-clustering
EM takes 0 mins minutes
Test cluster 4 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 5 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 6 for sub-clustering
EM takes 0 mins minutes
Test cluster 7 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 8 for sub-clustering
EM takes 0 mins minutes
Test cluster 9 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 10 for sub-clustering
EM takes 0 mins minutes
Test cluster 11 for sub-clustering
EM takes 0.017 mins minutes
Test cluster 12 for sub-clustering
EM takes 0.033 mins minutes
cluster 3 has 2 sub-cluster at 2, ICL=37
cluster 2 has 2 sub-cluster at 2, ICL=30
cluster 1 has 3 sub-cluster at 3, ICL=29
cluster 7 has 3 sub-cluster at 3, ICL=26
cluster 8 has 5 sub-cluster at 6, ICL=19
cluster 11 has 2 sub-cluster at 2, ICL=18
cluster 5 has 2 sub-cluster at 3, ICL=15
cluster 9 has 2 sub-cluster at 2, ICL=12
cluster 10 has 6 sub-cluster at 7, ICL=5.6
cluster 6 has 5 sub-cluster at 5, ICL=0.99
cluster 1 has 3 sub-cluster at 3, ICL=0
Model Refinement takes 0.15 mins minutes

Fit Model 8 of (6/10) K=12->12 N=9682
EM takes 0 mins minutes

Process completed at8

Major Iteration (Trans) (6/4) takes 0.53 mins minutes
> 
> ## apply asinh-transformation
> dat.fcs.transformed <- trans.ApplyToData(dat.res, dat.fcs)
> 
> ## plot results
> splom(dat.res, dat.fcs.transformed)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>