合并两个表，其中一列是 R 中另一列的子字符串答案

【问题标题】：Merging two tables where one column is substring of the other in R合并两个表，其中一列是 R 中另一列的子字符串
【发布时间】：2019-07-05 08:07:52
【问题描述】：

我有两个 data.frames，其中的列包含入藏号

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")

我想通过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 中的字符串的子字符串。

我考虑过使用fuzzyjoin，但很难正确匹配算法。

【问题讨论】：

标签： r merge fuzzyjoin

【解决方案1】：

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) 于 2019 年 3 月 17 日创建}

【讨论】：

不错，优雅的解决方案。将保留以备将来参考。谢谢！

【解决方案2】：

您可以使用sqldf 包并编写一个使用like 条件连接表的查询，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 || "%"
')

【讨论】：

因此，这实际上适用于左连接，但我想将所有行保留在 sub_df1 data.frame 中，当我尝试外连接时，我收到错误 RIGHT and FULL OUTER JOINs are not currently supported。有没有办法解决这个问题？
您可以将sub_df2 two left join sub_df1 one替换为sub_df1 one left join sub_df2 two
哈哈，你在打字的时候就这么做了……谢谢！