I want to clean up a taxonomy table with bacterial species in R and I want to delete values from all cells that start with the small letter.
I have a column from taxonomy df:
| Species |
|---|
| Tuwongella immobilis |
| Woesebacteria |
| unidentified marine |
| bacterium Ellin506 |
And I want:
| Species |
|---|
| Tuwongella immobilis |
| Woesebacteria |
unwanted <- "^[:upper:]+[:lower:]+"
tax.clean$Species <- str_replace_all(tax.clean$Species, unwanted, "")
but it doesn't seem to work and does not match desired species.
If you are working with dataframe, I suggest using dplyr::filter to clean up the dataframe.
grepl() returns logical values, !grepl(^[[:lower:]]) looks for anything that does not start with a lower case letter (^ indicate the beginning of a string).
library(dplyr)
df %>% filter(!grepl("^[[:lower:]]", Species))
Species
1 Tuwongella immobilis
2 Woesebacteria
We can do
grep('^[A-Z]', df$Species, value = T)
[1] "Tuwongella immobilis" "Woesebacteria"