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R (프로그래밍 언어) Bioconductor Vega #
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Software

Vega : Variational Segmentation for Copy Number Detection #

인간유전체프로젝트를 기점으로 방대한 데이터를 기반으로한 질병과의 연관성을 밝히는 연구가 활발히 진행되고 있다. Vega는 이러한 CNV(Copy Number Variantion)을 분석하는데 유용한 기능들을 제공하고 있다.

Example #

분석 방법을 알아보기 위해 Vega package에서 Example로 제공하는 Granta-519 Cell Line의 Log R Ratio(LRR)을 이용한 CNV 분석을 진행한다.

Code #

library(Vega)
data(G519)
G519[1:16,]
seg <- vega(CNVdata=G519, chromosomes=c(1:22,"X","Y"))
seg[1:5,]
plotSegmentation(G519, seg, chromosomes=c(1:22,"X","Y"), opt=0)
plotSegmentation(G519, seg, chromosomes=c("Y"), opt=0)

Data #

      Chromosome Probe Start Position Probe End Position LRR    
 [1,] "1"        "0"                  "0"                "0.02" 
 [2,] "1"        "0"                  "0"                "0.59" 
 [3,] "1"        "0"                  "0"                "0.09" 
 [4,] "1"        "0"                  "0"                "-0.1" 
 [5,] "1"        "0"                  "0"                "0.62" 
 [6,] "1"        "0"                  "0"                "-0.08"
 [7,] "1"        "50617"              "217280"           "0.12" 
 [8,] "1"        "722781"             "902347"           "0.17" 
 [9,] "1"        "851036"             "1037875"          "-0.13"
[10,] "1"        "899476"             "1049818"          "0.2"  
[11,] "1"        "946127"             "1096338"          "0.26" 
[12,] "1"        "1154648"            "1320545"          "-0.09"
[13,] "1"        "1286206"            "1419769"          "0.34" 
[14,] "1"        "1337829"            "1419769"          "0.36" 
[15,] "1"        "1501818"            "1681097"          "0.55" 
[16,] "1"        "1511518"            "1659697"          "0.45"

해당 Data는 각 Chromosome의 position에 해당하는 LRR 값을 보유하고 있다. 위 데이터를 Vega를 통해 특정 Regions의 CNV 상태를 결과로 보여준다

      Chromosome bp Start    bp End      Num of Markers Mean    Label
 [1,] "1"        "0"         "3098099"   "36"           "0.22"  "1"  
 [2,] "1"        "3103888"   "9047388"   "66"           "-0.24" "-1" 
 [3,] "1"        "9295827"   "10847085"  "18"           "0.11"  "0"  
 [4,] "1"        "10809955"  "33814729"  "253"          "-0.21" "-1" 
 [5,] "1"        "33732317"  "47694543"  "152"          "0.1"   "0"  
 [6,] "1"        "47577515"  "51935254"  "35"           "-0.3"  "-1" 
 [7,] "1"        "51864442"  "64839027"  "129"          "0.01"  "0"  
 [8,] "1"        "64741438"  "92888101"  "303"          "-0.3"  "-1" 
 [9,] "1"        "92709566"  "117738805" "266"          "-0.3"  "-1" 
[10,] "1"        "117623628" "149772257" "137"          "-0.03" "0"  
[11,] "1"        "149682654" "155624727" "66"           "0.1"   "0"  
[12,] "1"        "155622978" "161502227" "64"           "-0.32" "-1" 
[13,] "1"        "161615633" "171133937" "103"          "0.27"  "1"  
[14,] "1"        "171189854" "178190580" "68"           "0.03"  "0"  
[15,] "1"        "178079522" "187914826" "96"           "-0.27" "-1" 
[16,] "1"        "187901836" "226350085" "390"          "0.03"  "0"

Results #

  • All Chromosome

Image

  • Y Chromosome

Image

Suggested Pages #

0.0.1_20140628_0