重叠 data.table ||错误 y 的键必须与 by.y 中指定的列相同

Question

我有两个数据框。一个有两列，另一个有三列。第一个数据框有 SNP 名称及其位置。第二个三列数据框包含基因名称和基因起始和结束坐标的列。
我有兴趣根据边界执行连接。如果 SNP 落在基因边界内 return 它

dt_snp<-data.table("SNP"=c(paste("SNP",seq(1:10),sep="")), 
"BP"=c(1100, 89200, 2500, 33000, 5500, 69500, 12000,8800, 23200, 27000  )) ## SNP data

dt_gene<-data.table("GENE"=c("GENE1","GENE2","GENE3","GENE4","GENE5"), 
"START"=c(1000,2100,5000,40000,23000), "END"=c(2000,3000,9000,45000,30000)) ## Gene data

## do a join using data.table
snp_withingenes<-dt_snp[dt_gene, c("SNP","BP","GENE","START","END"), on=.(BP>=START, BP<=END), nomatch=0] # inner join

我用它得到了想要的结果，但是当我在存储在 R 包中的 R 脚本中执行此任务时，我收到 . 运算符的警告。警告如下：

 function_small: no visible global function definition for ‘.’
  Undefined global functions or variables:
    .

因此我想使用 foverlaps 但我很难理解它并用它达到预期的结果。这对我来说是违反直觉的

foverlaps(dt_snp,dt_gene, by.x=c("SNP","BP"), by.y=c("GENE","START","END"), nomatch=NA, type="any")

Error in foverlaps(dt_snp, dt_gene, by.x = c("SNP", "BP"), by.y = c("GENE",  : 
  The first 3 columns of y's key must be identical to the columns specified in by.y.

我应该如何获得所需的输出？

data.table_1.13.0 R v4.0 windows 平台

来自 devtools 的 check 对 R v4.0 rmarkdown_2.3 devtools_2.3.1 UNIX 平台

上的 . 操作员造成困扰

Answer 1

为了扩展我的评论，这里是 foverlaps 选项，它在两个 data.tables 中都需要两列，因此这里似乎不是最优的：

library(data.table)
dt_snp <- data.table("SNP"=c(paste("SNP",seq(1:10),sep="")), 
                   "BP"=c(1100, 89200, 2500, 33000, 5500, 69500, 12000,8800, 23200, 27000  )) ## SNP data

dt_gene <- data.table("GENE"=c("GENE1","GENE2","GENE3","GENE4","GENE5"), 
                    "START"=c(1000,2100,5000,40000,23000), "END"=c(2000,3000,9000,45000,30000)) ## Gene data
setkey(dt_gene, START, END)

dt_snp[, BP2 := BP]
## do a join using data.table
dt_snp[dt_gene, c("SNP","BP","GENE","START","END"), on=list(BP2 >= START, BP2 <= END), nomatch=0][]
#>      SNP    BP  GENE START   END
#> 1:  SNP1  1100 GENE1  1000  2000
#> 2:  SNP3  2500 GENE2  2100  3000
#> 3:  SNP5  5500 GENE3  5000  9000
#> 4:  SNP8  8800 GENE3  5000  9000
#> 5:  SNP9 23200 GENE5 23000 30000
#> 6: SNP10 27000 GENE5 23000 30000

setkey(dt_snp, BP, BP2)
foverlaps(dt_snp,dt_gene, by.x=c("BP", "BP2"), by.y=c("START","END"), nomatch=NULL, type="any")[, BP2 := NULL][]
#>     GENE START   END   SNP    BP
#> 1: GENE1  1000  2000  SNP1  1100
#> 2: GENE2  2100  3000  SNP3  2500
#> 3: GENE3  5000  9000  SNP5  5500
#> 4: GENE3  5000  9000  SNP8  8800
#> 5: GENE5 23000 30000  SNP9 23200
#> 6: GENE5 23000 30000 SNP10 27000

^{由 reprex package (v0.3.0)}

于 2020-08-06 创建

重叠 data.table ||错误 y 的键必须与 by.y 中指定的列相同

foverlaps data.table || error y's key must be identical to the columns specified in by.y

r

data.table

devtools