Extract the Chr number from the column-CodePudding

I have a data frame that has a column containing the chromosome details (1 to 22). I would like to create another column with only Chr numbers

CodePudding user response：

Please find below a solution with the package data.table:

REPREX

Code

library(data.table)
library(stringr)

DT[, Chr_ID := lapply(.SD, str_extract,"(?<=^chr)\\d "), .SDcols = "chromosome"]

Output

DT
#>              chromosome Chr_ID
#>  1: chr6_GL000253v2_alt      6
#>  2: chr6_GL000254v2_alt      6
#>  3: chr6_GL000255v2_alt      6
#>  4: chr6_GL000256v2_alt      6
#>  5:                chr4      4
#>  6:               chr11     11
#>  7:                chr8      8
#>  8:               chr12     12
#>  9:                chr2      2
#> 10:               chr12     12
#> 11:                chr4      4
#> 12:                chr6      6
#> 13:               chr15     15
#> 14:                chr4      4
#> 15:                chr2      2

Your data

DT <- data.table(chromosome = c("chr6_GL000253v2_alt", "chr6_GL000254v2_alt",
                 "chr6_GL000255v2_alt", "chr6_GL000256v2_alt", "chr4", "chr11",
                 "chr8", "chr12", "chr2", "chr12", "chr4", "chr6", "chr15", "chr4",
                 "chr2"))
DT
#>              chromosome
#>  1: chr6_GL000253v2_alt
#>  2: chr6_GL000254v2_alt
#>  3: chr6_GL000255v2_alt
#>  4: chr6_GL000256v2_alt
#>  5:                chr4
#>  6:               chr11
#>  7:                chr8
#>  8:               chr12
#>  9:                chr2
#> 10:               chr12
#> 11:                chr4
#> 12:                chr6
#> 13:               chr15
#> 14:                chr4
#> 15:                chr2

^{Created on 2021-10-12 by the}