Getting a sub string from a vector of strings

Question

I have a vector of strings

ids <- c("NM_006690.2_PROBE1","333212.1_PROBE1","7602049CB1_PROBE1","NM_018065.1_PROBE1","1539036CB1_PROBE1","NM_021019.1_PROBE1","1440608CB1_PROBE1","NM_031270.1_PROBE1","613678CB1_PROBE1")

A lot of discussing is already here: extract a substring in R according to a pattern.

I want to remove everything after a dot(.) and want to remove all after _ before PROBE. i managed to remove . by

read.table(text = ids, sep = ".", as.is = TRUE, fill=TRUE)$V1

I now mind to remove the _ before PROBE in cases like 613678CB1_PROBE1 and the output i want is 613678CB1 . How to do it.

Output:

"NM_006690", "333212"  , "7602049CB1"  "NM_018065","1539036CB1"  "NM_021019" "1440608CB1"  "NM_031270","613678CB1")

Note: There are two _'s one attached with NM and other with PROBE. I want the one every thing to be removed _PROBE

It would be better if you post the expected output. For the first case, do you need `NM_` — akrun, Apr 30 '15 at 16:48
Also please test your code before posting it. The `ids <- ` line has syntax errors. — G. Grothendieck, Apr 30 '15 at 16:50
The error is what you get when you enter the erroneous code into R but it seems someone has fixed the question for you. — G. Grothendieck, Apr 30 '15 at 17:00

A5C1D2H2I1M1N2O1R2T1 · Accepted Answer · 2015-04-30T17:05:02.800

6

It seems like you're asking for:

gsub("\\..*|_PROBE.*", "", ids)

Demo:

gsub("\\..*|_PROBE.*", "", ids)
# [1] "NM_006690"  "333212"     "7602049CB1" "NM_018065"  "1539036CB1"
# [6] "NM_021019"  "1440608CB1" "NM_031270"  "613678CB1"

edited Apr 30 '15 at 17:05

answered Apr 30 '15 at 16:56

A5C1D2H2I1M1N2O1R2T1

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grrgrrbla · Answer 2 · 2015-04-30T16:54:29.657

2

do you just want this?

ids <- c("NM_006690.2_PROBE1", "333212.1_PROBE1"  , "7602049CB1_PROBE1" , "NM_018065.1_PROBE1",
         "1539036CB1_PROBE1",  "NM_021019.1_PROBE1", "1440608CB1_PROBE1",  "NM_031270.1_PROBE1",
         "613678CB1_PROBE1")
ids <- read.table(text = ids, sep = ".", as.is = TRUE, fill=TRUE)$V1

library(stringr)
ids <- str_replace(ids, "_PROBE1", "")

which gives you this:

"NM_006690"  "333212"     "7602049CB1" "NM_018065"  "1539036CB1" "NM_021019"  "1440608CB1" "NM_031270"  "613678CB1"

edited Apr 30 '15 at 16:54

answered Apr 30 '15 at 16:51

grrgrrbla

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@akrun, I don't think that the OP has posted correct input or output data. – A5C1D2H2I1M1N2O1R2T1 Apr 30 '15 at 16:53
yeah there is one more step in between which he does, so the first two lines are actually the input-data with the transformation the op did beforehand... I edited my post – grrgrrbla Apr 30 '15 at 16:54

Getting a sub string from a vector of strings

2 Answers2

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