r语言 - 重叠数据表||错误 Y 的键必须与 by.y 中指定的列相同

Question

我有两个数据帧。一个有两列，另一个有三列。第一个数据帧具有SNP名称及其位置。具有三列的第二个数据帧具有具有基因名称以及基因的起始和结束坐标的列
我有兴趣执行基于边界的联接。如果SNP落在基因边界内，则返回

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

我用它得到了所需的结果，但当我在存储在R包中的R脚本中执行此任务时，我会收到.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实现期望的结果。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_1.13.0R v4.0windows平台

devtools中的check让R v4.0rmarkdown_2.3devtools_2.3.1UNIX平台上的.操作员感到烦恼

Answer 1

为了扩展我的评论，这里有foverlaps选项，它需要在两个data.tables中都有两列，因此在这里似乎不太理想：

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包(v0.3.0(于2020-08-06创建}