Extracting specific strings patterns from one column

Question

I would like to extract specific strings with the pattern gene=something from one column in R.

An example of input:

df <- 'V1 
       ID=gene92;DbX;gene=BH1;genePro
       ID=gene91;DbY;gene=BH2;genePro;inf2
       ID=gene90;DbY;gene=BH3;genePro;inf2'
df <- read.table(text=df, header=T)

The example of the expected output:

dfout <- 'V1 
         gene=BH1
         gene=BH2
         gene=BH3'
    dfout <- read.table(text=dfout, header=T)

Some idea to accomplish that?

Sotos · Accepted Answer · 2016-04-05 14:11:33Z

4

library(stringr)
str_extract(df$V1, 'gene=BH[0-9]+')
#[1] "gene=BH1" "gene=BH2" "gene=BH3"

answered Apr 5, 2016 at 14:11

Sotos

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2 Comments

Gopala Over a year ago

Assuming gene names could be variable and not always be BH and number, you could try str_extract(df$v1, 'gene=(.*?);') and gsub out that semicolon?

Sotos Over a year ago

I just went with the example. It can of course be more generalized via sub

Julius Vainora · Accepted Answer · 2019-02-05 14:56:16Z

1

You may also use

gsub(".*(gene=.*?)(;|$).*", "\\1", df$V1)
# [1] "gene=BH1" "gene=BH2" "gene=BH3"

so that we match only the part gene=... that follows anything, .*, and is followed by ; or the end of the string, ;|$.

edited Feb 5, 2019 at 14:56

answered Apr 5, 2016 at 14:19

Julius Vainora

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