Mutlistep Cleaning/Regex: Substitution & Extract Portion Before Separator [on hold]

Mutlistep Cleaning Regex: Substitution & Extract Portion Before Separator.R

library(tidyverse)

as.data.frame(M, stringsAsFactors = FALSE) %>%
    rownames_to_column('id') %>%
    mutate(
        id = gsub('SuperSMART_', 'S', id), 
        id = gsub('(^S)(\\d{2})(_)', '\\10\\2\\3', id, perl = TRUE) 
    ) %>%
    separate(id, into = c('S', 'R', 'p'), sep = '_', remove = FALSE) %>%  
    mutate(., group = group_indices(., S))

##             id    S  R    p x group
## 1 S003_T1_p555 S003 T1 p555 1     1
## 2 S003_T2_p456 S003 T2 p456 2     1
## 3 S004_T3_p785 S004 T3 p785 3     2
## 4 S004_T4_p426 S004 T4 p426 4     2
## 5 S027_T1_p112 S027 T1 p112 5     3
## 6 S027_T2_p414 S027 T2 p414 6     3
## 7 S042_T3_p155 S042 T3 p155 7     4
## 8 S042_T5_p775 S042 T5 p775 8     4


## If you really want it as a function:
normalize_data <- function(m, ..) {
    as.data.frame(m, stringsAsFactors = FALSE) %>%
        tibble::rownames_to_column('id') %>%
        dplyr::mutate(
            id = gsub('SuperSMART_', 'S', id), 
            id = gsub('(^S)(\\d{2})(_)', '\\10\\2\\3', id, perl = TRUE) 
        ) %>%
        tidyr::separate(id, into = c('S', 'R', 'p'), sep = '_', remove = FALSE) %>%  
        dplyr::mutate(., group = dplyr::group_indices(., S))
}

Hi Tyler. Thanks for this solution again. can you please explain the gsub('(^S)(\d{2})(_)', '\10\2\3', id, perl = TRUE) line?
I think I understand what has been done in all other lines.
Regards

So this is a groupped capture denoted by the parenthesis '(^S)(\d{2})(_)'. There are 3 groups being captured. 1: (^S), 2:(\d{2}), 3: (_). The first one says grab from the beginning (^) and S. The second group says grab after that where there are exactly 2 digits (\\d{2}) and then the 3rd group says it must be followed by an underscore.

So S27_T2_p414 would be matched by this but S004_T3_p785 would not.

For the replacment of '\10\2\3'....If it matches '(^S)(\d{2})(_)' we can use perl = TRUE to replace the group capturing (denoted by parenthesis above. The \1 corresponds to (^S) ; the \2 corresponds to (\d{2}) AND \3 goes with (_). We can insert things in between the capture groups. This technique is called backreference. In this case I insert an extra zero between the first capture group and the second to ensure all numbers have 3 digits. This makes an assumption that at most you have 3 digits in the string after S.