数据框查找值在范围内并返回不同的列

Question

我有两个数据帧,并希望使用one(DF1$pos)中的值来搜索DF2中的两列(DF2start,DF2end),如果它在这些数字范围内,则返回DF2$name

DF1

ID   pos  name
chr   12
chr  542
chr  674

DF2

ID   start   end   annot
chr      1   200      a1
chr    201   432      a2
chr    540  1002      a3
chr   2000  2004      a4

所以在这个例子中我希望DF1成为

ID   pos  name
chr   12    a1
chr  542    a3
chr  674    a3

我尝试过使用merge和intersect但不知道如何使用if带有逻辑表达式的语句.

数据帧应编码如下,

DF1  <- data.frame(ID=c("chr","chr","chr"),
               pos=c(12,542,672),
               name=c(NA,NA,NA))

DF2  <- data.frame(ID=c("chr","chr","chr","chr"),
               start=c(1,201,540,200),
               end=c(200,432,1002,2004),
               annot=c("a1","a2","a3","a4"))

Answer 1

也许你可以使用foverlaps"data.table"包.

library(data.table)
DT1 <- data.table(DF1)
DT2 <- data.table(DF2)
setkey(DT2, ID, start, end)
DT1[, c("start", "end") := pos]  ## I don't know if there's a way around this step...
foverlaps(DT1, DT2)
#     ID start  end annot pos i.start i.end
# 1: chr     1  200    a1  12      12    12
# 2: chr   540 1002    a3 542     542   542
# 3: chr   540 1002    a3 674     674   674
foverlaps(DT1, DT2)[, c("ID", "pos", "annot"), with = FALSE]
#     ID pos annot
# 1: chr  12    a1
# 2: chr 542    a3
# 3: chr 674    a3

正如@Arun在评论中所提到的,您还可以使用which = TRUEin foverlaps来提取相关值:

foverlaps(DT1, DT2, which = TRUE)
#    xid yid
# 1:   1   1
# 2:   2   3
# 3:   3   3
DT2$annot[foverlaps(DT1, DT2, which = TRUE)$yid]
# [1] "a1" "a3" "a3"