Question

我有两个数据框，希望在一个（DF1$pos）中使用该值来搜索DF2中的两列（DF2start，DF2end），如果它在这些数字范围内，则返回DF2$name < / p>

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但不知道如何使用带有逻辑表达式的if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＆＃34; data.table＆＃34;中的foverlaps。封装

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

如@Arun在评论中所述，您还可以使用which = TRUE中的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"

Answer 2

您也可以使用IRanges

source("http://bioconductor.org/biocLite.R")
biocLite("IRanges")
library(IRanges)
DF1N <- with(DF1, IRanges(pos, pos))
DF2N <- with(DF2, IRanges(start, end))
DF1$name <- DF2$annot[subjectHits(findOverlaps(DF1N, DF2N))]
DF1
#   ID pos name
#1 chr  12   a1
#2 chr 542   a3
#3 chr 674   a3

数据框查找值在范围内并返回不同的列

2 个答案: