This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Find similar values in two gene lists

Hi guys, I have two very large gene data sets, and I want to extract all the matching values that are in the two lists.

but I haven't been successful until now,

so far this is my code 

                  list1 = ("1_10.txt")
                  list2 = ("1_10.txt")

   ID <- match(list1,list2) 
          result1 <- list2[na.omit(ID)]
                   unique(result1)
                      write.csv(ID,file="matchedresults1.txt")




   list1 
        EnsemblGeneID
         ENSG00000109573
         ENSG00000205003
         ENSG00000124603
         ENSG00000008313
         ENSG00000183043
         ENSG00000179863
         ENSG00000141337
         ENSG00000154257

     list2 
        EnsemblGeneID
         ENSG00000109573
         ENSG00000205003
         ENSG00000124603
         ENSG00000008313
         ENSG00000183043
         ENSG00000179863
         ENSG00000141338
         ENSG00000154258

So I expected that see the extracted data: 

     list3 
        EnsemblGeneID
         ENSG00000109573
         ENSG00000205003
         ENSG00000124603
         ENSG00000008313
         ENSG00000183043
         ENSG00000179863

thanks for reading

r coding
• 2,300 views • link
updated by 2nelly 2nelly • written by Nicky • Nicky

intersect()

• 0 views • link
written by ATpoint ATpoint

Hi there, I have a long list of genes in two files.

Let me try your script

• 0 views • link
written by Nicky • Nicky

Nicky : Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

• 0 views • link
written by GenoMax GenoMax

3 answers 

 list1 
    EnsemblGeneID
     ENSG00000109573
     ENSG00000205003
     ENSG00000124603
     ENSG00000008313
     ENSG00000183043
     ENSG00000179863
     ENSG00000141337
     ENSG00000154257

 list2 
    EnsemblGeneID
     ENSG00000109573
     ENSG00000205003
     ENSG00000124603
     ENSG00000008313
     ENSG00000183043
     ENSG00000179863
     ENSG00000141338
     ENSG00000154258

 list1 
    EnsemblGeneID
     ENSG00000109573
     ENSG00000205003
     ENSG00000124603
     ENSG00000008313
     ENSG00000183043
     ENSG00000179863
     ENSG00000141337
     ENSG00000154257

 list2 
    EnsemblGeneID
     ENSG00000109573
     ENSG00000205003
     ENSG00000124603
     ENSG00000008313
     ENSG00000183043
     ENSG00000179863
     ENSG00000141338
     ENSG00000154258

So I expected that see the extracted data: 

 list3 
    EnsemblGeneID
     ENSG00000109573
     ENSG00000205003
     ENSG00000124603
     ENSG00000008313
     ENSG00000183043
     ENSG00000179863

thanks Again!

• 0 views • link
updated by ATpoint ATpoint • written by Nicky • Nicky

You have to add description as a comment and not as answer.

• 0 views • link
written by piyushjo piyushjo

Try this

list1<-read.delim("1_10.txt")
list2<-read.delim("1_10.txt")

Here both of your lists are exactly same. Do you have long list of genes in two files or is it a matrix? The following will work for a list with one column. First convert factors into characters array

list1<-as.character(list1) 
#If the read.delim makes list1 as a data.frame with 1 column, you would need as.character(list1$X), where X is the heading of column, or x if there was no heading. 
list2<-as.character(list2)    
keep<- list1%in%list2 
sel<- list1[keep] 
sel<-sel[!duplicated(sel)]
write.csv(sel,"matchedresults1.txt")
• 0 views • link
written by piyushjo piyushjo

Hi there, I have a long list of genes in two files.

I with your script I got the following result

                                      "","x"
                                      "1","1_10.txt"

no idea what does it mean :(

• 0 views • link
written by Nicky • Nicky

You first need to have files with those name in the folder. list1 and list2 are the two lists that have given in your example.

• 0 views • link
written by piyushjo piyushjo

You can try this

awk 'NR==FNR {end[$1]; next} ($1 in end)' list1 list2

In case you want to match different columns change the first $1 with the number of column you want to compare or the second $1 to match with another column

• 0 views • link
written by 2nelly 2nelly

Log in to answer this question.

More posts like this

No similar posts found.