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Question: About Package ‘clValid’
1
gravatar for mhorie25
4.6 years ago by
mhorie25 • 10
Japan
mhorie25 • 10 wrote:

Hi

I am trying to do "self-organizing tree algorithm" using Package ‘clValid’.

I practiced sample data (mouse), and I could do it.

However, I can not extract genes from each cluster.(for example, 45 genes from cluster2 in the following example )

If there are anybody familiar with this package, please teach me how to do it.

Thank you in advance!

Regards,

 

*********************************

library(clValid)                          
data(mouse)
express <- mouse[,c("M1","M2","M3","NC1","NC2","NC3")]
rownames(express) <- mouse$ID
sotaCl <- sota(as.matrix(express), 4)
names(sotaCl)
sotaCl
plot(sotaCl)
plot(sotaCl, cl=2)

 
rna-seq R gene • 1.3k views
ADD COMMENT • link •
modified 4.6 years ago • written 4.6 years ago by mhorie25 • 10
1
gravatar for dario.garvan
4.6 years ago by
dario.garvan • 430
Australia
dario.garvan • 430 wrote:

You should read the documentation for the function sota.

?sota

The result, sotaCl, has an element which has the cluster number of each sample.

sotaCl[["clust"]]
  [1] 1 2 2 1 1 2 2 1 2 2 5 2 1 4 2 1 4 5 2 1 2 1
 [23] 2 2 2 2 4 2 2 2 1 4 2 1 1 2 2 2 1 2 1 5 4 2
 [45] 2 5 2 2 2 2 1 2 5 4 2 1 2 2 1 2 2 4 1 2 2 2
 [67] 1 5 1 3 3 1 3 1 1 5 3 3 1 5 1 4 3 1 1 3 5 1
 [89] 3 1 3 3 3 3 3 3 3 3 3 1 3 3 3 3 3 3 5 3 3 3
[111] 3 3 1 3 1 3 5 5 3 3 1 1 4 3 1 3 3 3 1 1 1 1
[133] 1 3 3 3 3 3 3 1 1 3 3 5 1 3 3

To get the genes in each cluster,

split(1:length(sotaCl[["clust"]]), sotaCl[["clust"]])
$`1`
 [1]   1   4   5   8  13  16  20  22  31  34  35
[12]  39  41  51  56  59  63  67  69  72  74  75
[23]  79  81  84  85  88  90 100 113 115 121 122
[34] 125 129 130 131 132 133 140 141 145

$`2`
 [1]  2  3  6  7  9 10 12 15 19 21 23 24 25 26 28
[16] 29 30 33 36 37 38 40 44 45 47 48 49 50 52 55
[31] 57 58 60 61 64 65 66

$`3`
 [1]  70  71  73  77  78  83  86  89  91  92  93
[12]  94  95  96  97  98  99 101 102 103 104 105
[23] 106 108 109 110 111 112 114 116 119 120 124
[34] 126 127 128 134 135 136 137 138 139 142 143
[45] 146 147

$`4`
[1]  14  17  27  32  43  54  62  82 123

$`5`
 [1]  11  18  42  46  53  68  76  80  87 107 117
[12] 118 144
ADD COMMENT • link written 4.6 years ago by dario.garvan • 430
0
gravatar for mhorie25
4.6 years ago by
mhorie25 • 10
Japan
mhorie25 • 10 wrote:

Dear Dario Garvan

Thank you very much!

 
ADD COMMENT • link written 4.6 years ago by mhorie25 • 10
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