合并两个表，其中一列是 R 中另一列的子字符串

Question

我有两个 data.frames 列包含登录号

df 1 的子集：

sub_df1 <- structure(list(database = "CLO, ArrayExpress, ArrayExpress, ATCC, BCRJ, BioSample, CCLE, ChEMBL-Cells, ChEMBL-Targets, Cosmic, Cosmic, Cosmic, Cosmic-CLP, GDSC, GEO, GEO, GEO, IGRhCellID, LINCS_LDP, Wikidata", 
    database_accession = "CLO_0009006, E-MTAB-2770, E-MTAB-3610, CRL-7724, 0337, SAMN03471142, SH4_SKIN, CHEMBL3308177, CHEMBL2366309, 687440, 909713, 2159447, 909713, 909713, GSM887568, GSM888651, GSM1670420, SH4, LCL-1280, Q54953204"), .Names = c("database", 
"database_accession"), row.names = 2L, class = "data.frame")

df 2 的子集：

sub_df2 <- structure(list(database_accession = "SH4_SKIN", G1 = -1.907138, 
    G2 = -7.617305, G3 = -3.750553, G4 = 2.615004, G5 = 9.751557), .Names = c("database_accession", 
"G1", "G2", "G3", "G4", "G5"), row.names = 101L, class = "data.frame")

我想按 database_accession 列合并两个数据框，但问题是它们不完全匹配。 sub_df2 中的字符串是 sub_df1.

中字符串的子字符串

我考虑过使用 fuzzyjoin，但很难找到正确的匹配算法。

Answer 1

您可以使用 sqldf 包并编写一个查询，使用 like 条件连接表，以测试 sub_df1 中的值是否包含 sub_df2 中的值.

library(sqldf)
sqldf('
select  *
from    sub_df2 two
        left join sub_df1 one
          on one.database_accession like "%" || two.database_accession || "%"
')

Answer 2

fuzzyjoin解决方案，使用match_fun = str_detect或regex_join():

library(tidyverse); library(fuzzyjoin)
# Load data
sub_df1 <- structure(list(database = "CLO, ArrayExpress, ArrayExpress, ATCC, BCRJ, BioSample, CCLE, ChEMBL-Cells, ChEMBL-Targets, Cosmic, Cosmic, Cosmic, Cosmic-CLP, GDSC, GEO, GEO, GEO, IGRhCellID, LINCS_LDP, Wikidata", database_accession = "CLO_0009006, E-MTAB-2770, E-MTAB-3610, CRL-7724, 0337, SAMN03471142, SH4_SKIN, CHEMBL3308177, CHEMBL2366309, 687440, 909713, 2159447, 909713, 909713, GSM887568, GSM888651, GSM1670420, SH4, LCL-1280, Q54953204"), .Names = c("database", "database_accession"), row.names = 2L, class = "data.frame")
sub_df2 <- structure(list(database_accession = "SH4_SKIN", G1 = -1.907138, G2 = -7.617305, G3 = -3.750553, G4 = 2.615004, G5 = 9.751557), .Names = c("database_accession", "G1", "G2", "G3", "G4", "G5"), row.names = 101L, class = "data.frame")

# Solution
# Using fuzzy_join. Could also use regex_full_join(), which is the wrapper for match_fun = str_detect, mode = "full"
fuzzy_join(sub_df1, sub_df2, match_fun = str_detect, by = "database_accession", mode = "full") %>% 
  str()
#> 'data.frame':    1 obs. of  8 variables:
#>  $ database            : chr "CLO, ArrayExpress, ArrayExpress, ATCC, BCRJ, BioSample, CCLE, ChEMBL-Cells, ChEMBL-Targets, Cosmic, Cosmic, Cos"| __truncated__
#>  $ database_accession.x: chr "CLO_0009006, E-MTAB-2770, E-MTAB-3610, CRL-7724, 0337, SAMN03471142, SH4_SKIN, CHEMBL3308177, CHEMBL2366309, 68"| __truncated__
#>  $ database_accession.y: chr "SH4_SKIN"
#>  $ G1                  : num -1.91
#>  $ G2                  : num -7.62
#>  $ G3                  : num -3.75
#>  $ G4                  : num 2.62
#>  $ G5                  : num 9.75

^{由 reprex package (v0.2.1)}

创建于 2019-03-17

合并两个表，其中一列是 R 中另一列的子字符串

Merging two tables where one column is substring of the other in R

merge

r

fuzzyjoin