由于特定的正则表达式，如何使用 mutate(across()) 更改列？

Question

我对 mutate(across()) 函数有疑问。在下面的标题中，我想删除列中的“字母+下划线”（例如“p__”、“c__”等）。

A tibble: 2,477 x 4
   Phylum                Class                   Order               Family                 
   <chr>                 <chr>                   <chr>               <chr>                  
 1 " p__Proteobacteria"  " c__Gammaproteobacter~ " o__Aeromonadales" " f__Aeromonadaceae"   
 2 " p__Bacteroidota"    " c__Bacteroidia"       " o__Bacteroidales" " f__Williamwhitmaniac~
 3 " p__Fusobacteriota"  " c__Fusobacteriia"     " o__Fusobacterial~ " f__Leptotrichiaceae" 
 4 " p__Firmicutes"      " c__Clostridia"        " o__Clostridiales" " f__Clostridiaceae"   
 5 " p__Proteobacteria"  " c__Gammaproteobacter~ " o__Enterobactera~ " f__Enterobacteriacea~
 6 " p__Bacteroidota"    " c__Bacteroidia"       " o__Bacteroidales" " f__Williamwhitmaniac~
 7 " p__Firmicutes"      " c__Clostridia"        " o__Lachnospirale~ " f__Lachnospiraceae"  
 8 " p__Bacteroidota"    " c__Bacteroidia"       " o__Cytophagales"  " f__Spirosomaceae"    
 9 " p__Proteobacteria"  " c__Gammaproteobacter~ " o__Burkholderial~ " f__Comamonadaceae"   
10 " p__Actinobacteriot~ " c__Actinobacteria"    " o__Frankiales"    " f__Sporichthyaceae"  
# ... with 2,467 more rows

一年前我用过命令

table <- table %>% 
  mutate_at(vars(Phylum, Class, Order, Family),funs(sub(pattern = "^([a-z])(_{2})", replacement = "", .)))

现在，它提示我 funs-function 不再受支持并且不再有效。你对我有什么建议吗？我考虑过：

taxon <- c("Phylum", "Class", "Order", "Family")
table <- table %>% 
  mutate(across(taxon), gsub(pattern = "^([a-z])(_{2})", replacement = "", .))

但是我得到了错误：

Error: Invalid index: out of bounds

非常感谢:) 凯瑟琳

Answer 1

你可以这样做：

library(dplyr)

taxon <- c("Phylum", "Class", "Order", "Family")
table <- table %>%  mutate(across(taxon, 
          ~gsub(pattern = "^([a-z])(_{2})", replacement = "", .)))

我没有你的数据来证实这一点，但字符串开头似乎有一个空格，应该先将其删除。

table <- table %>%  mutate(across(taxon, 
           ~gsub(pattern = "^([a-z])(_{2})", replacement = "", trimws(.))))

由于特定的正则表达式，如何使用 mutate(across()) 更改列？

How can I change columns with mutate(across()) due to a specific RegEx?

r

dplyr

across