This is a method for Allele-specific DNA Copy Number Profiling using NGS.

입력형식은 다음과 같다.

> head(readMatrix)
  AT BT AN BN
1 32 38 17 23
2 34 25 27 23
3 49 47 19 16
4 39 44 28 26
5 40 46 34 29
6 31 48 22 31

AT: A allele at tumor, BT: B allele at tumor를 의미한다. 이를 위해서는 GATK등으로 VCF를 만들고 이로 부터 각 SNV의 allele를 depth로 부터 위 행렬을 만들어야 한다.

주요 함수들

• getChangepoints: 한쪽 혹은 양쪽 copy number가 바뀌는 위치를 알려준다. (CBS 알고리즘 사용)
• gatASCN: ASCN을 알려준다.

ASCN 결과는 다음과 같다

"CHROM" "start" "end"   "AT"    "BT"    "AN"    "BN"    "cns1"  "cns2"
"1"     "chr1"  1       808922  2       16      3       15      0.833884202991642       1
"2"     "chr1"  808923  3750731 0       25      0       35      0.265226002470057       0.413876122026238
"3"     "chr1"  3750732 7399646 0       8       0       15      0.482943003639532       1
"4"     "chr1"  7399647 11293959        0       17      0       25      0.841592396660685       1.20543455215355

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[Medical Scholarly Articles] About (MedicalScholarlyArticle 0) #

• Allele-specific copy number profiling by next-generation DNA sequencing

Related Medical Scholarly Articles (MedicalScholarlyArticle 1) #

• Allele-specific copy number profiling by next-generation DNA sequencing
• Gene-based comparative analysis of tools for estimating copy number alterations using whole-exome sequencing data

Related Articles (Article 2) #

• Allele-specific copy number
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