Renaming columns if a specific character string doesn't exist

Question

I'm looking to rename colnames to include the characters _16S_sed if they're not present. For example I have the dataset

> dput(dataframe1)
structure(list(GL11_DN_1_16S_sed = structure(1:3, .Label = c("val1", 
"val2", "val3"), class = "factor"), GL12_UP_3_16S_sed = structure(1:3, .Label = c("val1", 
"val2", "val3"), class = "factor"), GL13_1_DN = structure(1:3, .Label = c("val1", 
"val2", "val3"), class = "factor")), class = "data.frame", row.names = c(NA, 
-3L))

where the third column needs the characters _16S_sed. TIA

jpsmith · Accepted Answer · 2023-06-29 13:50:27Z

3

In base R, one approach would be to first identify the columns missing the desired string using grep or grepl, then replace:

missing_colnames <- grep("_16S_sed", colnames(df), invert = TRUE) # thanks @rps1227
colnames(df)[missing_colnames] <- paste0(colnames(df[missing_colnames]), "_16S_sed")

# or
missing_colnames2 <- !grepl("_16S_sed", colnames(df))
colnames(df)[missing_colnames2] <- paste0(colnames(df)[missing_colnames2], "_16S_sed")

Output:

#   GL11_DN_1_16S_sed GL12_UP_3_16S_sed GL13_1_DN_16S_sed
# 1              val1              val1              val1
# 2              val2              val2              val2
# 3              val3              val3              val3

edited Jun 29, 2023 at 13:50

answered Jun 29, 2023 at 13:12

jpsmith

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2 Comments

rps1227 Over a year ago

You can use invert = TRUE in grep() to get the indices that do not containt 16S_sed instead of setdiff() too.

jpsmith Over a year ago

@rps1227 thanks! Excellent point - I have edited accordingly

HoelR · Accepted Answer · 2023-06-29 13:09:14Z

2

library(tidyverse)

df %>%  
  rename_with(~ if_else(str_detect(.x, "_16S_sed"), .x, str_c(.x, "_16S_sed")))

# A tibble: 3 × 3
  GL11_DN_1_16S_sed GL12_UP_3_16S_sed GL13_1_DN_16S_sed
  <fct>             <fct>             <fct>            
1 val1              val1              val1             
2 val2              val2              val2             
3 val3              val3              val3

Glimpsed:

Rows: 3
Columns: 3
$ GL11_DN_1_16S_sed <fct> val1, val2, val3
$ GL12_UP_3_16S_sed <fct> val1, val2, val3
$ GL13_1_DN_16S_sed <fct> val1, val2, val3

answered Jun 29, 2023 at 13:09

HoelR

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