CODEWITHSUNDEEP
rformatgsub
bry.cop
bry.cop

Reputation: 3

gsub producing a range rather than desired expression in R

I would like to read in a table then use gsub to return a part of the text. I know gsub requires a character vector format. Instead of getting the desired samp list of 'C516_A1_B1' and pat list of'C516' etc, I get'1:5'. What is the simplest way to fix this? Thanks!

bamlist <- read.table('pathtotxtfile.txt')

for (y in bamlist) {
    samp <- gsub('EPICC_(C\\S+)_S1\\S+$','\\1', bamlist)
    pat <- gsub('(C\\d+)_\\S+$','\\1', samp)
}

bamlist:

EPICC_C516_A1_B1_S1-GRCh38.bam
EPICC_C516_A1_G4_S1-GRCh38.bam
EPICC_C516_B1_G7_S1-GRCh38.bam
EPICC_C516_B1_G8_S1-GRCh38.bam
EPICC_C516_B3_B1_S1-GRCh38.bam

Upvotes: 0

Views: 62

Answers (1)

Rui Barradas
Rui Barradas

Reputation: 76402

Why loop, sub is vectorized over x.

samp <- sub("^[^_]*_(.*)_[^_]*$", "\\1", bamlist)
pat <- sub("(^[^_]+)_.*$", "\\1", samp)

samp
#[1] "C516_A1_B1" "C516_A1_G4" "C516_B1_G7" "C516_B1_G8"
#[5] "C516_B3_B1"
pat
#[1] "C516" "C516" "C516" "C516" "C516"

Data

bamlist <- scan(what = character(), text = "
EPICC_C516_A1_B1_S1-GRCh38.bam
EPICC_C516_A1_G4_S1-GRCh38.bam
EPICC_C516_B1_G7_S1-GRCh38.bam
EPICC_C516_B1_G8_S1-GRCh38.bam
EPICC_C516_B3_B1_S1-GRCh38.bam
")

Edit

Following user @akrun's comment, here is a way to apply the above code to a data.frame.

lapply(bamlist, function(y){
  samp <- sub("^[^_]*_(.*)_[^_]*$", "\\1", y)
  pat <- sub("(^[^_]+)_.*$", "\\1", samp)
  data.frame(samp = samp, pat = pat)
})
#$X
#        samp  pat
#1 C516_A1_B1 C516
#2 C516_A1_G4 C516
#3 C516_B1_G7 C516
#4 C516_B1_G8 C516
#5 C516_B3_B1 C516

The data would now be

X <- scan(what = character(), text = "
EPICC_C516_A1_B1_S1-GRCh38.bam
EPICC_C516_A1_G4_S1-GRCh38.bam
EPICC_C516_B1_G7_S1-GRCh38.bam
EPICC_C516_B1_G8_S1-GRCh38.bam
EPICC_C516_B3_B1_S1-GRCh38.bam
")

bamlist <- data.frame(X)

Upvotes: 2

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