CODEWITHSUNDEEP
r
Stacey John
Stacey John

Reputation: 151

column wise clustering in R

I have the data matrix in the following way:

ID_REF GSM362180    GSM362181  GSM362188    GSM362189  GSM362192
244901 5.094871713 4.626623079 4.554272515 4.748604391 4.759221647
244902 5.194528083 4.985930299 4.817426064 5.151654407 4.838741605
244903 5.412329253 5.352970877 5.06250609  5.305709079 8.365082403
244904 5.529220594 5.28134657  5.467445095 5.62968933  5.458388909
244905 5.024052699 4.714631878 4.792865831 4.843975286 4.657188246
244906 5.786557533 5.242403911 5.060605782 5.458148567 5.890061836

I would like to cluster it column-wise to find out the similar promoters( columns represent the promoters and the rows - the genes). I used pv clust to do it earlier but would like to have a more detailed clustering ( maybe with hierarchial type ?). I would like to know how far the columns cluster together. I have in total 20 columns and 22810 genes.

Upvotes: 0

Views: 818

Answers (1)

Paul Hiemstra
Paul Hiemstra

Reputation: 60924

Googling for R clustering yields a host of interesting results. An option could be hclust. This link might also be interesting.

Upvotes: 1

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