How to split gene names in my list?

Question

[Parham]

Hi,

I am working in R environment and I have a long list of gene names which I am showing few first objects of it here:

[1] SPNCRNA.1436,omh5,snR95
[2] snR46
[3] snR10
[4] SPNCRNA.1651,SPNCRNA.515
[5] snR42
[6] SPNCRNA.1094,SPNCRNA.1095,SPRRNA.47,SPRRNA.48
[7] snR88
[8] SPNCRNA.497
[9] SPSNORNA.54
[10] snoR39b

I am wondering if there is any way to split the indexes with several gene names in them into individual ones? The list is so long.

Thanks!

Answer 1

[TriS]

to elaborate a little on RamRS answer:

x <- c("SPNCRNA.1436,omh5,snR95","snR46", "snR10", "SPNCRNA.1651,SPNCRNA.515")
results <- c()
for (i in 1:length(x)){
  n <- 1
  xi <- strsplit(x[i], ",")
  results <- c(results, xi[[1]][n])
  # print(xi[[1]][n], sep="")
  while (!is.na(xi[[1]][n+1])){
    n <- n+1
    # print(xi[[1]][n], sep="")
    results <- c(results, xi[[1]][n])
  }
}

results
[1] "SPNCRNA.1436" "omh5"         "snR95"        "snR46"        "snR10"        "SPNCRNA.1651" "SPNCRNA.515"

--added some edits--

RamRS already gave you a perfect code, I still modified mine above

with this you can then save the results in whichever way you prefer.

x is your initial vector with the names, if it's part of a column then x will be myMatrix[,(# col with x)] or myDataFrame$x

[Parham]

Thanks for your time writing the code. The thing is the gene list contains about 500 entries and I need to apply it to whole list. Besides the gene names are not alternative names of one gene. So only splitting them would be enough. I appreciate if you could give some help on that.

[Ram]

I've just added more details on my answer. HTH.

[TriS]

added some edits too, it can handle any number of entries, no matter if 10 or 500

[Parham]

Thank you guys both. Sorry for replying late. I've been caught up with some stuff.

The code you showed me was a big lesson.

Cheers!

Answer 2

[Ram]

You can sapply with strsplit to split each element of the vector by ,

Edit: Sorry, I was half asleep when I wrote this answer, so could not test code before posting it here. I've now added the logic behind my solution, code and output.

Logic:

Apply strsplit on each element of the vector and flatten the resulting list of vectors using unlist.

Code:

> x <- c("SPNCRNA.1436,omh5,snR95","snR46", "snR10", "SPNCRNA.1651,SPNCRNA.515","SPNCRNA.1094,SPNCRNA.1095,SPRRNA.47,SPRRNA.48")
> listOfSplitStringVectors<-sapply(x,function(i) strsplit(i,",")
> flattenedVectorOfNames=unlist(listOfSplitStringVectors,recursive = TRUE,use.names = FALSE)

Output:

[1] "SPNCRNA.1436" "omh5"         "snR95"        "snR46"        "snR10"       
[6] "SPNCRNA.1651" "SPNCRNA.515"  "SPNCRNA.1094" "SPNCRNA.1095" "SPRRNA.47"   
[11] "SPRRNA.48"