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Last data update: 2014.03.03

R: Extract the posterior probabilities of response from a MIMOSA...

getZ	R Documentation

Extract the posterior probabilities of response from a MIMOSA model

Description

Extract the posterior probabilities of response from a MIMOSA model

Extract the component weights from a MIMOSA model

Usage

getZ(x)

## S3 method for class 'MIMOSAResultList'
getZ(x)

## S3 method for class 'MIMOSAResult'
getZ(x)

getW(x)

## S3 method for class 'MIMOSAResultList'
getW(x)

## S3 method for class 'MIMOSAResult'
getW(x)

Arguments

`x`	output from a MIMOSA model

Value

a matrix of posterior probabilities

a vector of component weights

Examples

data(ICS)
E<-ConstructMIMOSAExpressionSet(ICS,
  reference=ANTIGEN%in%'negctrl',measure.columns=c('CYTNUM','NSUB'),
  other.annotations=c('CYTOKINE','TCELLSUBSET','ANTIGEN','UID'),
  default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET,
  .variables=.(TCELLSUBSET,CYTOKINE,UID),
  featureCols=1,ref.append.replace='_REF')

result<-MIMOSA(NSUB+CYTNUM~UID+TCELLSUBSET+CYTOKINE|ANTIGEN,
    data=E, method='EM',
    subset=RefTreat%in%'Treatment'&ANTIGEN%in%'ENV',
    ref=ANTIGEN%in%'ENV'&RefTreat%in%'Reference')
    getZ(result)
data(ICS)
E<-ConstructMIMOSAExpressionSet(ICS,
  reference=ANTIGEN%in%'negctrl',measure.columns=c('CYTNUM','NSUB'),
  other.annotations=c('CYTOKINE','TCELLSUBSET','ANTIGEN','UID'),
  default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET,
  .variables=.(TCELLSUBSET,CYTOKINE,UID),
  featureCols=1,ref.append.replace='_REF')

result<-MIMOSA(NSUB+CYTNUM~UID+TCELLSUBSET+CYTOKINE|ANTIGEN,
    data=E, method='EM',
    subset=RefTreat%in%'Treatment'&ANTIGEN%in%'ENV',
    ref=ANTIGEN%in%'ENV'&RefTreat%in%'Reference')
getW(result)

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(MIMOSA)
Loading required package: MASS
Loading required package: plyr
Loading required package: reshape

Attaching package: 'reshape'

The following objects are masked from 'package:plyr':

    rename, round_any

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ggplot2

This is package 'modeest' written by P. PONCET.
For a complete list of functions, use 'library(help = "modeest")' or 'help.start()'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MIMOSA/MIMOSA-accessors.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getZ
> ### Title: Extract the posterior probabilities of response from a MIMOSA
> ###   model
> ### Aliases: getW getW.MIMOSAResult getW.MIMOSAResultList getZ
> ###   getZ.MIMOSAResult getZ.MIMOSAResultList
> 
> ### ** Examples
> 
> data(ICS)
> E<-ConstructMIMOSAExpressionSet(ICS,
+   reference=ANTIGEN%in%'negctrl',measure.columns=c('CYTNUM','NSUB'),
+   other.annotations=c('CYTOKINE','TCELLSUBSET','ANTIGEN','UID'),
+   default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET,
+   .variables=.(TCELLSUBSET,CYTOKINE,UID),
+   featureCols=1,ref.append.replace='_REF')
> 
> result<-MIMOSA(NSUB+CYTNUM~UID+TCELLSUBSET+CYTOKINE|ANTIGEN,
+     data=E, method='EM',
+     subset=RefTreat%in%'Treatment'&ANTIGEN%in%'ENV',
+     ref=ANTIGEN%in%'ENV'&RefTreat%in%'Reference')
Warning message:
In .local(formula, data, ...) :
  Formula does not contain the RefTreat variable. It will be added automatically. Set RT=FALSE to disable this.
>     getZ(result)
                          Pr.Nonresponse Pr.response
1_ENV_IFNg_CD4_Treatment    1.000000e+00  0.00000000
1_ENV_TNF_CD4_Treatment     1.000000e+00  0.00000000
1_ENV_IL2_CD4_Treatment     9.824234e-01  0.01757658
2_ENV_IFNg_CD4_Treatment    8.827129e-01  0.11728714
2_ENV_TNF_CD4_Treatment     1.000000e+00  0.00000000
2_ENV_IL2_CD4_Treatment     9.829209e-01  0.01707909
3_ENV_IFNg_CD4_Treatment    3.536033e-01  0.64639668
3_ENV_TNF_CD4_Treatment     6.984997e-01  0.30150033
3_ENV_IL2_CD4_Treatment     9.824234e-01  0.01757658
4_ENV_IFNg_CD4_Treatment    1.000000e+00  0.00000000
4_ENV_TNF_CD4_Treatment     1.000000e+00  0.00000000
4_ENV_IL2_CD4_Treatment     1.000000e+00  0.00000000
5_ENV_IFNg_CD4_Treatment    1.000000e+00  0.00000000
5_ENV_TNF_CD4_Treatment     1.000000e+00  0.00000000
5_ENV_IL2_CD4_Treatment     4.782255e-01  0.52177452
6_ENV_IFNg_CD4_Treatment    5.736120e-01  0.42638798
6_ENV_TNF_CD4_Treatment     9.550749e-01  0.04492506
6_ENV_IL2_CD4_Treatment     9.958351e-01  0.00416487
7_ENV_IFNg_CD4_Treatment    9.829209e-01  0.01707909
7_ENV_TNF_CD4_Treatment     1.000000e+00  0.00000000
7_ENV_IL2_CD4_Treatment     9.829209e-01  0.01707909
8_ENV_IFNg_CD4_Treatment    1.000000e+00  0.00000000
8_ENV_TNF_CD4_Treatment     6.984997e-01  0.30150033
8_ENV_IL2_CD4_Treatment     9.824234e-01  0.01757658
9_ENV_IFNg_CD4_Treatment    1.000000e+00  0.00000000
9_ENV_TNF_CD4_Treatment     1.000000e+00  0.00000000
9_ENV_IL2_CD4_Treatment     1.000000e+00  0.00000000
10_ENV_IFNg_CD4_Treatment   9.423974e-01  0.05760256
10_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
10_ENV_IL2_CD4_Treatment    1.000000e+00  0.00000000
11_ENV_IFNg_CD4_Treatment   9.829209e-01  0.01707909
11_ENV_TNF_CD4_Treatment    4.645457e-01  0.53545435
11_ENV_IL2_CD4_Treatment    7.908779e-01  0.20912209
12_ENV_IFNg_CD4_Treatment   7.682250e-01  0.23177500
12_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
12_ENV_IL2_CD4_Treatment    6.984997e-01  0.30150033
13_ENV_IFNg_CD4_Treatment   9.824234e-01  0.01757658
13_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
13_ENV_IL2_CD4_Treatment    1.000000e+00  0.00000000
14_ENV_IFNg_CD4_Treatment   7.908779e-01  0.20912209
14_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
14_ENV_IL2_CD4_Treatment    9.958351e-01  0.00416487
15_ENV_IFNg_CD4_Treatment   8.336719e-01  0.16632811
15_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
15_ENV_IL2_CD4_Treatment    1.000000e+00  0.00000000
16_ENV_IFNg_CD4_Treatment   8.926461e-01  0.10735394
16_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
16_ENV_IL2_CD4_Treatment    1.000000e+00  0.00000000
17_ENV_IFNg_CD4_Treatment   1.000000e+00  0.00000000
17_ENV_TNF_CD4_Treatment    8.827129e-01  0.11728714
17_ENV_IL2_CD4_Treatment    9.958351e-01  0.00416487
18_ENV_IFNg_CD4_Treatment   9.240638e-01  0.07593623
18_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
18_ENV_IL2_CD4_Treatment    1.000000e+00  0.00000000
19_ENV_IFNg_CD4_Treatment   8.336719e-01  0.16632811
19_ENV_TNF_CD4_Treatment    8.336719e-01  0.16632811
19_ENV_IL2_CD4_Treatment    1.000000e+00  0.00000000
20_ENV_IFNg_CD4_Treatment   9.829209e-01  0.01707909
20_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
20_ENV_IL2_CD4_Treatment    9.150162e-01  0.08498383
21_ENV_IFNg_CD4_Treatment   1.000000e+00  0.00000000
21_ENV_TNF_CD4_Treatment    9.958351e-01  0.00416487
21_ENV_IL2_CD4_Treatment    1.000000e+00  0.00000000
22_ENV_IFNg_CD4_Treatment   1.000000e+00  0.00000000
22_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
22_ENV_IL2_CD4_Treatment    9.423974e-01  0.05760256
23_ENV_IFNg_CD4_Treatment   9.581739e-01  0.04182607
23_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
23_ENV_IL2_CD4_Treatment    1.000000e+00  0.00000000
24_ENV_IFNg_CD4_Treatment   1.000000e+00  0.00000000
24_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
24_ENV_IL2_CD4_Treatment    1.000000e+00  0.00000000
25_ENV_IFNg_CD4_Treatment   9.550749e-01  0.04492506
25_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
25_ENV_IL2_CD4_Treatment    8.926461e-01  0.10735394
26_ENV_IFNg_CD4_Treatment   8.662913e-01  0.13370867
26_ENV_TNF_CD4_Treatment    5.072861e-02  0.94927139
26_ENV_IL2_CD4_Treatment    3.111928e-06  0.99999689
27_ENV_IFNg_CD4_Treatment   8.336719e-01  0.16632811
27_ENV_TNF_CD4_Treatment    8.131860e-01  0.18681404
27_ENV_IL2_CD4_Treatment    4.311005e-10  1.00000000
28_ENV_IFNg_CD4_Treatment   8.373263e-01  0.16267367
28_ENV_TNF_CD4_Treatment    7.114246e-02  0.92885754
28_ENV_IL2_CD4_Treatment    4.204602e-01  0.57953977
29_ENV_IFNg_CD4_Treatment   2.405958e-01  0.75940419
29_ENV_TNF_CD4_Treatment    6.402921e-06  0.99999360
29_ENV_IL2_CD4_Treatment    1.336568e-06  0.99999866
30_ENV_IFNg_CD4_Treatment   7.114246e-02  0.92885754
30_ENV_TNF_CD4_Treatment    3.833105e-01  0.61668952
30_ENV_IL2_CD4_Treatment    4.563989e-08  0.99999995
31_ENV_IFNg_CD4_Treatment   3.015652e-01  0.69843478
31_ENV_TNF_CD4_Treatment    1.754294e-01  0.82457055
31_ENV_IL2_CD4_Treatment    4.411419e-01  0.55885814
32_ENV_IFNg_CD4_Treatment   5.736120e-01  0.42638798
32_ENV_TNF_CD4_Treatment    1.731429e-01  0.82685711
32_ENV_IL2_CD4_Treatment    2.947900e-10  1.00000000
33_ENV_IFNg_CD4_Treatment   1.731429e-01  0.82685711
33_ENV_TNF_CD4_Treatment    6.984997e-01  0.30150033
33_ENV_IL2_CD4_Treatment    1.060254e-07  0.99999989
34_ENV_IFNg_CD4_Treatment   6.288888e-01  0.37111118
34_ENV_TNF_CD4_Treatment    5.880287e-04  0.99941197
34_ENV_IL2_CD4_Treatment    8.526513e-13  1.00000000
35_ENV_IFNg_CD4_Treatment   7.114246e-02  0.92885754
35_ENV_TNF_CD4_Treatment    1.520919e-02  0.98479081
35_ENV_IL2_CD4_Treatment    1.457582e-04  0.99985424
36_ENV_IFNg_CD4_Treatment   3.696601e-01  0.63033992
36_ENV_TNF_CD4_Treatment    1.000000e+00  0.00000000
36_ENV_IL2_CD4_Treatment    1.728072e-04  0.99982719
37_ENV_IFNg_CD4_Treatment   9.240638e-01  0.07593623
37_ENV_TNF_CD4_Treatment    4.645457e-01  0.53545435
37_ENV_IL2_CD4_Treatment    3.718696e-10  1.00000000
38_ENV_IFNg_CD4_Treatment   7.712187e-01  0.22878132
38_ENV_TNF_CD4_Treatment    3.380742e-03  0.99661926
38_ENV_IL2_CD4_Treatment    1.082645e-03  0.99891736
39_ENV_IFNg_CD4_Treatment   9.150162e-01  0.08498383
39_ENV_TNF_CD4_Treatment    9.344393e-05  0.99990656
39_ENV_IL2_CD4_Treatment    3.336983e-02  0.96663017
40_ENV_IFNg_CD4_Treatment   9.581739e-01  0.04182607
40_ENV_TNF_CD4_Treatment    3.943879e-05  0.99996056
40_ENV_IL2_CD4_Treatment    5.737215e-07  0.99999943
41_ENV_IFNg_CD4_Treatment   9.550749e-01  0.04492506
41_ENV_TNF_CD4_Treatment    9.865278e-05  0.99990135
41_ENV_IL2_CD4_Treatment    1.578883e-09  1.00000000
42_ENV_IFNg_CD4_Treatment   1.585238e-05  0.99998415
42_ENV_TNF_CD4_Treatment    2.875831e-03  0.99712417
42_ENV_IL2_CD4_Treatment    5.630487e-03  0.99436951
43_ENV_IFNg_CD4_Treatment   1.731429e-01  0.82685711
43_ENV_TNF_CD4_Treatment    6.327018e-01  0.36729817
43_ENV_IL2_CD4_Treatment    1.578883e-09  1.00000000
44_ENV_IFNg_CD4_Treatment   1.731429e-01  0.82685711
44_ENV_TNF_CD4_Treatment    4.211118e-03  0.99578888
44_ENV_IL2_CD4_Treatment    1.676607e-02  0.98323393
45_ENV_IFNg_CD4_Treatment   2.482732e-04  0.99975173
45_ENV_TNF_CD4_Treatment    3.743983e-02  0.96256017
45_ENV_IL2_CD4_Treatment    2.046363e-12  1.00000000
46_ENV_IFNg_CD4_Treatment   8.362933e-01  0.16370674
46_ENV_TNF_CD4_Treatment    6.290533e-04  0.99937095
46_ENV_IL2_CD4_Treatment    8.917027e-10  1.00000000
47_ENV_IFNg_CD4_Treatment   1.818684e-01  0.81813158
47_ENV_TNF_CD4_Treatment    9.180255e-02  0.90819745
47_ENV_IL2_CD4_Treatment    1.312110e-05  0.99998688
48_ENV_IFNg_CD4_Treatment   1.000000e+00  0.00000000
48_ENV_TNF_CD4_Treatment    4.130457e-03  0.99586954
48_ENV_IL2_CD4_Treatment    1.057953e-06  0.99999894
49_ENV_IFNg_CD4_Treatment   8.336719e-01  0.16632811
49_ENV_TNF_CD4_Treatment    2.033035e-02  0.97966965
49_ENV_IL2_CD4_Treatment    6.089826e-06  0.99999391
50_ENV_IFNg_CD4_Treatment   8.336719e-01  0.16632811
50_ENV_TNF_CD4_Treatment    1.818684e-01  0.81813158
50_ENV_IL2_CD4_Treatment    5.484168e-04  0.99945158
> data(ICS)
> E<-ConstructMIMOSAExpressionSet(ICS,
+   reference=ANTIGEN%in%'negctrl',measure.columns=c('CYTNUM','NSUB'),
+   other.annotations=c('CYTOKINE','TCELLSUBSET','ANTIGEN','UID'),
+   default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET,
+   .variables=.(TCELLSUBSET,CYTOKINE,UID),
+   featureCols=1,ref.append.replace='_REF')
> 
> result<-MIMOSA(NSUB+CYTNUM~UID+TCELLSUBSET+CYTOKINE|ANTIGEN,
+     data=E, method='EM',
+     subset=RefTreat%in%'Treatment'&ANTIGEN%in%'ENV',
+     ref=ANTIGEN%in%'ENV'&RefTreat%in%'Reference')
> getW(result)
                ENV
w.nonresp 0.5936961
w.resp    0.4063039
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>