R语言实现结构突变数据的整合

BiocManager::install("intansv")

1. 读取breakDancer的函数参数设置：

##读取breakDancer的预测结果，并进行预处理
breakdancer.file.path<-system.file("extdata/ZS97.breakdancer.sv",package="intansv")
breakdancer<- readBreakDancer(breakdancer.file.path)

##读取cnvnator结果
cnvnator.dir.path<- system.file("extdata/cnvnator", package="intansv")
cnvnator <-readCnvnator(cnvnator.dir.path)

##读取SVseq2的结果
svseq.dir.path<- system.file("extdata/svseq2", package="intansv")
svseq <-readSvseq(svseq.dir.path)

##DELLY结果提取
delly.file.path<- system.file("extdata/ZS97.DELLY.vcf",package="intansv")
delly <-readDelly(delly.file.path)

##Pindel结果的提取
pindel.dir.path<- system.file("extdata/pindel", package="intansv")
pindel <-readPindel(pindel.dir.path)

##Lumpy数据的提取
lumpy.file.path<-system.file("extdata/ZS97.LUMPY.vcf",package="intansv")
lumpy <-readLumpy(lumpy.file.path)

##SoftSearch结果提取
softSearch.file.path<- system.file("extdata/ZS97.softsearch",package="intansv")
softSearch<- readSoftSearch(softSearch.file.path)

###结果的整合
sv_all_methods<- methodsMerge(breakdancer, pindel, cnvnator, delly, svseq)

###突变的注释，会分别注释三种结构突变
anno.file.path<- system.file("extdata/chr05_chr10.anno.txt",package="intansv")
msu_gff_v7<- read.table(anno.file.path, head=TRUE, as.is=TRUE)

sv_all_methods.anno<- llply(sv_all_methods,svAnnotation,genomeAnnotation=msu_gff_v7)

###基因组层面的可视化
genome.file.path<- system.file("extdata/chr05_chr10.genome.txt",package="intansv")
genome <-read.table(genome.file.path, head=TRUE, as.is=TRUE)

plotChromosome(genome,sv_all_methods,1000000)

###区域的可视化
plotRegion(sv_all_methods,msu_gff_v7,"chr05", 1, 200000)