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Table of Contents
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
- Y Chromosome
Suggested Pages #
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- 0.025 normalization
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