Use a regular expression extract substring from data frame columns in R

Question

I am fairly new to R so please go easy on me if this is a stupid question.

I have a dataframe called foo :

< head(foo)
  Old.Clone.Name New.Clone.Name                                  File
1         A          Aa           A_mask_MF_final_IS2_SAEE7-1_02.nrrd
2         B          Bb   B_mask_MF_final_IS2ViaIS2h_SADQ15-1_02.nrrd
3         C          Cc   C_mask_MF_final_IS2ViaIS2h_SAEC16-1_02.nrrd
4         D          Dd    D_mask_MF_final_IS2ViaIS2h_SAEJ6-1_02.nrrd
5         E          Ee           F_mask_MF_final_IS2_SAED9-1_02.nrrd
6         F          Ff    F_mask_MF_final_IS2ViaIS2h_SAGP3-1_02.nrrd

I want to extract codes from the File column that match the regular expression (S[AZ]{3}[0-9]{1,2}-[0-9]_02) , to give me:

SAEE7-1_02
SADQ15-1_02
SAEC16-1_02
SAEJ6-1_02
SAED9-1_02
SAGP3-1_02

I then want to use these codes to search another directory for other files that contain the same code.

I fail, however, at the first hurdle and cannot extract the codes from that column of the data frame.

I have tried:

library('stringr')
str_extract(foo[3],regex("(S[A-Z]{3}[0-9]{1,2}-[0-9]_02)", ignore_case = TRUE))

but this just returns [1] NA .

Am I simply missing something obvious? I look forward to cracking this with a bit of help from the community.

Answer 1

Hello if you are reading the data as a table file then foo[3] is a list and str_extract does not accept lists, only strings, then you should use lapply to extract the match of every element.

lapply(foo[3], function(x) str_extract(x, "[sS][a-zA-Z]{3}[0-9]{1,2}-[0-9]_02"))

Result:

[1] "SAEE7-1_02"  "SADQ15-1_02" "SAEC16-1_02" "SAEJ6-1_02"  "SAED9-1_02"
[6] "SAGP3-1_02"

Answer 2

str_extract(foo[3],"(?i)S[A-Z]{3}[0-9]{1,2}-[0-9]_02")

seems to work. Somehow, my R gave me

"Error in check_pattern(pattern, string) : could not find function "regex""

when using your original expression.

Answer 3

The following code will repeat what you asked (just copy and paste to your R console ):

library(stringr)
foo = scan(what='')
Old.Clone.Name New.Clone.Name File
A Aa A_mask_MF_final_IS2_SAEE7-1_02.nrrd
B Bb B_mask_MF_final_IS2ViaIS2h_SADQ15-1_02.nrrd
C Cc C_mask_MF_final_IS2ViaIS2h_SAEC16-1_02.nrrd
D Dd D_mask_MF_final_IS2ViaIS2h_SAEJ6-1_02.nrrd
E Ee F_mask_MF_final_IS2_SAED9-1_02.nrrd
F Ff F_mask_MF_final_IS2ViaIS2h_SAGP3-1_02.nrrd


foo = matrix(foo,ncol=3,byrow=T)
colnames(foo)=foo[1,]
foo = foo[-1,]
foo
str_extract(foo[,3],regex("(S[A-Z]{3}[0-9]{1,2}-[0-9]_02)", ignore_case = T))

The reason you get NULL is hidden: R stores entries by column, hence foo[3] is the 3rd row and 1st column of foo matrix/data frame. To quote the third column, you may need to use foo[,3] . or foo<-data.frame(foo); foo[[3]] foo<-data.frame(foo); foo[[3]] .