CODEWITHSUNDEEP
rgrepl
Rea Kalampaliki
Rea Kalampaliki

Reputation: 164

How to use grepl function multiple times, in R

I have a vector like go_id and a data.frame like data.

go_id <- c("[GO:0000086]", "[GO:0000209]", "[GO:0000278]")


protein_id <- c("Q96IF1","P26371","Q8NHG8","P60372","O75526","Q01130")
bio_process <- c("[GO:0000086]; [GO:0000122]; [GO:0000932]", "[GO:0005829]; [GO:0008544]","[GO:0000209]; [GO:0005737]; [GO:0005765]","NA","[GO:0000398]; [GO:0003729]","[GO:0000278]; [GO:0000381]; [GO:0000398]; [GO:0003714]")
data <- as.data.frame(cbind(protein_id,bio_process))

How can I keep the rows of the data for which bio_process cell contains at least one of the go_ids elements? I note that the GO code can not be repeated in the same bio_process cell.

To be more precise, i would like to receive only the first, the third and the sixth row of the data.frame.

I have tried a for loop using 'grepl' function, like this:

go_id <- gsub("GO:","", go_id, fixed = TRUE)
for (i in 1:6) {
  new_data <- data[grepl("\\[GO:go_id[i]\\]",data$Gene.ontology..biological.process.)]
  }

Which I know it can not work because I can not fit in a variable value into a regular expression.

Any ideas on this? Thank you

Upvotes: 1

Views: 202

Answers (3)

Chris Ruehlemann
Chris Ruehlemann

Reputation: 21400

You can subset using str_extract to define the pattern on those substrings that are distinctive: 

library(stringr)
data[grepl(paste(str_extract(go_id, "\\d{4}]"), collapse="|"),  data$bio_process),]
  protein_id                                            bio_process
1     Q96IF1               [GO:0000086]; [GO:0000122]; [GO:0000932]
3     Q8NHG8               [GO:0000209]; [GO:0005737]; [GO:0005765]
6     Q01130 [GO:0000278]; [GO:0000381]; [GO:0000398]; [GO:0003714]

EDIT:

The most straighforward solution is subsetting with grepland paste0 to add the escape slashes for the metacharacter [:

data[grepl(paste0("\\", go_id, collapse="|"),  data$bio_process),]

Upvotes: 1

Samuel Allain
Samuel Allain

Reputation: 479

You should use fixed = TRUE in grepl() :

vect <- rep(FALSE, nrow(data))
for(id in go_id){
  vect <- vect | grepl(id, data$bio_process, fixed = T)
}
data[vect,]

Upvotes: 1

akrun
akrun

Reputation: 887148

We can use Reduce with grepl

data$ind <-  Reduce(`|`, lapply(go_id, function(pat) 
           grepl(pat, data$bio_process, fixed = TRUE)))

data
#  protein_id                                            bio_process   ind
#1     Q96IF1               [GO:0000086]; [GO:0000122]; [GO:0000932]  TRUE
#2     P26371                             [GO:0005829]; [GO:0008544] FALSE
#3     Q8NHG8               [GO:0000209]; [GO:0005737]; [GO:0005765]  TRUE
#4     P60372                                                     NA FALSE
#5     O75526                             [GO:0000398]; [GO:0003729] FALSE
#6     Q01130 [GO:0000278]; [GO:0000381]; [GO:0000398]; [GO:0003714]  TRUE

Upvotes: 1

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