Matrices and data frames are write different. For this you most likely want to 
use days frames.

?merge

Using typical options merge gives you all columns from both data frames. You 
can choose to select specific columns by indexing the data frames before 
passing them to merge if you don't want that.
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On September 9, 2015 12:39:43 PM PDT, Lida Zeighami <lid.z...@gmail.com> wrote:
>Hi there,
>
>I want to find the intersection between two different data frame or
>matrices based on two columns.
>for example in matrix A I have 5 columns, the first two columns are Id1
>and
>Id2 and I have the same columns in the other matrix B, (Id1, Id2 ,,,)
>how can I find the intersection between these two matrices based on
>columns
>Id1 and Id2 in R?
>
>Thanks
>
>       [[alternative HTML version deleted]]
>
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>and provide commented, minimal, self-contained, reproducible code.

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