compare two data frames column to column

Question

[MAPK]

Hi everyone,

I have two csv files where the content of one file is in other file, but not in exactly same column/row position. The headers and IDs are same, but the corresponding contents are not always same. Is there any way I can look for each ID/header content of one file into another and see if they are same. I would prefer this in R, but not sure how to get this done. Please advise.

Thank you.

Here are the files and I want to see where exactly they differ.

File1

    mpk    mkk    mkkk   Rdh    Jak
1    5,6    22,22    18,19    20,20    50,40
2    10,19   12,14  19,22    34,50    40,44
3    11,13    15,16    22,22    50,50    34,38

File 2

   mpk    mkk    mkkk   Rdh    Jak
1    8,8   11,11    18,19    20,20    50,40
2    10,19   12,14  19,22    16,18    40,44
3    11,13    15,16    22,22    50,50    3,3

[Michael]

This is not a bioinformatics problem, especially with the example given!

[MAPK]

OK I changed it. Here is the actual problem. I made that old example to make you guys understand.

[Sam]

So basically, you are trying to see if two particular column from two different file, disregarding their title, whether if they are the same?

Answer 1

[Josh Herr]

In addition to Sam's answer, this can be done pretty easily in R with the merge function or with plyr. I agree this example is not a bioinformatics question, but I recently had to do this for RNA-Seq count data, so I understand how you could use it.

These two answers are not bioinformatics specific, but they should help you:

1. How do I combine two data-frames based on two columns?
2. Merge a lot of data frames in R

Answer 2

[Sam]

If I understand you correctly, you are trying to do the following:

e.g. File A contains content of File B

All columns in File B can be found in File A

You want to find that for each column in File A that can be found in File B, whether if the content is the same. If that is the case, you can do the following assuming in R

A = read.table("FileA", header=T)
B = read.table("FileB", header=T)

for(i in ncol(B)){
  correspondingACol  = grep(colnames(B)[i] , colnames(A))
  A[,correspondingACol]%in%B[,i] #True means the content in A can be found in B.
}

If however, you want to match multiple columns, e.g. it is only considered as a match if and only if all columns in B can be found in A, then I guess you can use the merge function