[英]How to merge two data frames by matching two numeric columns with a +-5 range?
我有兩個數據框如下:
df1 <- data.frame(chrom = c(1,1,3,6,6),
chromStart = c(15433, 1959,34205,35043, 77456),
chromEnd = c(15700, 2001,36245,36245,78469),
id = c('aaad', 'dfk', 'bb', 'llk', 'ie9o'))
df2 <- data.frame(chrom = c(1,1,5,1,6),
chromStart2 = c(15433, 1961,34205,1962, 77456),
chromEnd2 = c(15700, 2002,36245,1999,78480))
我想通過匹配chrom == chrom, chromStart = between(chromStart2 -5, chromStart2 +5)
和chromEnd = between(chromEnd2 -5, chromEnd2 +5)
來合並兩個數據幀。 我試過的是:
library(dplyr)
colnames(df2) <- c('chrom','chromStart', 'chromEnd')
merged <- inner_join(df1,df2)
然而,這只匹配精確的chromStart
和chromEnd
,在我們的例子中只有aaad
匹配。 我想給它一個加號或減號的范圍,以便dfk
匹配。 我的實際數據幀是 260000 行和 179000 行,所以如果可能的話我更喜歡 memory 有效的方法。 以下是我正在尋找的結果:
data.frame(chrom = c(1,1,1),
chromStart = c(15433, 1959,1959),
chromEnd = c(15700, 2001,2001),
id = c('aaad', 'dfk', 'dfk'),
chromStart2 = c(15433, 1961,1962),
chromEnd2 = c(15700, 2002,1999))
可能有更好/更有效的方法,但這些方法應該有效。
dplyr
方法:根據您的條件創建兩個臨時邏輯向量,然后根據滿足這兩個條件的那些filter
s,然后刪除 ( select
) 臨時列:
merged <- inner_join(df1, df2) %>%
mutate(
inStart = chromStart >= chromStart2 - 5 & chromStart <= chromStart2 + 5,
inEnd = chromEnd >= chromEnd2 - 5 & chromEnd <= chromEnd + 5) %>%
filter(inStart, inEnd) %>%
select(-inStart, -inEnd)
### or in one `mutate` command:
# merged <- inner_join(df1, df2) %>%
# mutate(inrows = (chromStart >= chromStart2 - 5 & chromStart <= #chromStart2 + 5) &
# (chromEnd >= chromEnd2 - 5 & chromEnd <= chromEnd + 5)) %>%
# filter(inrows) %>%
# select(-inrows)
Output:
# chrom chromStart chromEnd id chromStart2 chromEnd2
# 1 1 15433 15700 aaad 15433 15700
# 2 1 1959 2001 dfk 1961 2002
# 3 1 1959 2001 dfk 1962 1999
並檢查以確保它完全符合最終所需的數據:
all.equal(merged,
data.frame(chrom = c(1,1,1),
chromStart = c(15433, 1959,1959),
chromEnd = c(15700, 2001,2001),
id = c('aaad', 'dfk', 'dfk'),
chromStart2 = c(15433, 1961,1962),
chromEnd2 = c(15700, 2002,1999))
)
# [1] TRUE
base R
方法:通過識別滿足相同條件的行來對數據進行子集化
base1 <- merge(df1, df2, by = "chrom")
base_merged <- base1[(base1$chromStart >= base1$chromStart2 - 5 & base1$chromStart <= base1$chromStart2 + 5) &
(base1$chromEnd >= base1$chromEnd2 - 5 & base1$chromEnd <= base1$chromEnd + 5),]
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