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How to extract OTU count information for the selected list of OTU in R

Hi,

Could you please suggest to me in R, how I can extract count information across all samples for the selected list of OTU ID from the OTU table where the first column is OTU ID.

I have identified some differential OTU abundance and now for heatmap, I need the count information for these OTU across all samples.

r
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written by Bioinfonext Bioinfonext

You cannot (and should not) ask for direct answers. Show us what you have tried so far. Also, don't assume that everyone will know what an OTU table is ; rather provide a snapshot of how the table looks like. for example you can provide

summary(OTU_TABLE) or str(OTU_TABLE) or head(OTU_TABLE)

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written by lakhujanivijay lakhujanivijay

thanks, sorry for that: I do have OTU Id in first column and sample count like this, I need to extract information for based on selected OTU ids.

> head( mymensingh2)
                                          leaf-1.S68     leaf-19.S79
673b8e48866a5fdd473f09ad34e0b2c0              5                 3
b72e8a63316f0378c695f8050a87166d              0                 4
85f5b8db1099500c61fc3881b5e44a75              7                 0
ad224d08bb86a6f85854d7894ec973c8              0                 6
71f84e7910006f22684121564206e8ca              0                 0
3a0d6d1e61954036684c9d7056e9b7c1              0                 0

I do have long list of this data but here suppose if I need information only for like these below OTU ID how i can do this in R:

673b8e48866a5fdd473f09ad34e0b2c0                               
b72e8a63316f0378c695f8050a87166d                   
85f5b8db1099500c61fc3881b5e44a75

Thanks for your help. Bioinfonext

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written by Bioinfonext Bioinfonext

Dear Vijay,

Thanks, could you please suggest now, how I can do the filtering for required list of OTU ID in R?

Thanks Bioinfornext

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written by Bioinfonext Bioinfonext

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