How to combine items from two columns in two separate files? - r

Question

I have two tables which I need to compare
Table 1:XLOC IDs
Column A: Xloc id
Column B: gene id
Table 2: Ensembl IDs
Column A: Ensembl id
Column B: gene Id
In both tables, there are identical Gene ids (names e.g. cpa6). In table 1 there are 25000 entries, in table 2 there are 46000 entries.
I need to insert the Ensemble Ids from ColA, Table 2 into ColC of Table1, when both gene ids in column B match and create an output file with new data- e.g.
Table 1
ENS0002 cpa6
Table 2:
Xloc0014 cpa6
Output file, Table 3:
ENS0002 cpa6 Xloc0014
The columns are not in the same order and cannot be sorted alphabetically etc. The remaining 21000 entries without corresponding Xlocs I will get rid of (but can easily do this post-output).
Does anyone know how to do this in either R, Excel, or other software?, relatively easily?
N.B. Both tables can not be sorted into the same order, so I really need to use a formula/script/bash to do this.

Answer 1

Try this. I have created an example data frame to show how you can merge and keep only the values that exist in both tables.
As you can see the new table is a result of these values that exist in both and now you have 3 columns with the value of the second table.
In case you want to keep all the rows that exist in both you must use the column gene Id in order to keep these gene Id that exist in both.newTable <- merge(tab1,tab2,by = "gen_id") for example.
tab1 <- data.frame(col1=c("id1","id2","id3","id4"),col2=c(1,2,3,4))
tab2 <- data.frame(col1=c("id1","id2","id3","id5","id7"),col2=c(1,3,3,5,6))
newTable <- merge(tab1,tab2,by = "col1")
in case you want to keep all from table1 but maybe they dont exist in table2 use this.
newTable <- merge(tab1,tab2,by = "col1",all.x=T)
these will keep all the rows of table1 and will give a value at col2.y otherwise you will have NAs.

Answer 2

In R I would use the merge function merge(Table 1, Table 2,by="cpa6").
However, I have done this in Excel before, which worked well too using the VLOOKUP function. You just need to use a IF function in R, with a nested VLOOKUP inside:
=IF(ISERROR(VLOOKUP(cell with gene name in Table1,array of cells that contain the gen names in Table2, number of the column in the array in Table2,"TRUE" so they match exactly)), Output if true, output if false).
Example:
=IF(ISERROR(VLOOKUP(C4,List1!A1:List1!A$2:A$1000,1,TRUE)), "Does NOT exist in List 1","Exists in List 1")