[R] Overlapping Matrices By column correlation

[David Winsemius]

On Jan 8, 2015, at 2:26 AM, Karim Mezhoud wrote:

> Mantel test is interesting but it can't displays wish columns are similar.
> 
> Here an example:  M
>                        gene1   gene2  gene3  gene4   gene5
> Sample1           2            4            1           7            2
> Sample2          0               NA        2.3      1            9
> Sample3
> ......
> 
> M1, M2, M3 are three matrices of genes expression from three diseases.
> genes in columns and samples in rows.
> I would like to know which diseases has nearest gene expression profile to
> others? and which genes are in common?

Two things we need:

1) Reproducible example: Perhaps dput(list( M1[1:10,1:10) , M2[ 1:10.1:10] ))

2) A suggested metric for distance between such data objects that would be acceptable to practitioners in whatever dark arts this activity is being conducted

> Any suggestion?
> Thanks
> Karim
> 
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> and provide commented, minimal, self-contained, reproducible code.

-- 

David Winsemius
Alameda, CA, USA