#Masked Copy Number Segment, 此表是在上面数据上过滤掉了一些与生殖和性染色体相关的数据。
#Copy Number Segmentation， 得到一个基因区间和此区间的拷贝数的表，共6列。最后一列Segment_Mean值就是 log2(copy_number/ 2), 正常来说人是二倍体生物则此value值为0，如果拷贝数小于2（删除）则小于0，拷贝数大于2（扩增）则大于0.
query <- GDCquery(project = "TCGA-STAD",
data.category = "Copy Number Variation",
data.type = "Gene Level Copy Number", # Gene Level Copy Number , Masked Copy Number Segment,Copy Number Segment
#workflow.type = "STAR - Counts", # 数据已经合并 可以直接提取
#sample.type = sample_type,
legacy = FALSE)
GDCdownload(query )
cnv.data <- GDCprepare(query )
write.table(data.frame(cnv.data,check.names = F), file ="cnv.tsv", sep="\t",row.names =F, quote = F)
