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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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How study co-occurence between two independant kingdom with phyloseq ? #1468

Open KLequette opened 3 years ago

KLequette commented 3 years ago

Hi,

I'm looking for study rhizosphere microbiote (fungi and bacteria) in R. I have two independent sequencing data (bacteria & fungi) and I would like to perform co-occurence analysis. I use phyloseq package but it is not clear if we can do this with phyloseq. Anyone did it ? If yes, how did you do ?

Cheers !

Fungi phyloseq-class experiment-level object otu_table() OTU Table: [ 214 taxa and 342 samples ] sample_data() Sample Data: [ 342 samples by 5 sample variables ] tax_table() Taxonomy Table: [ 214 taxa by 7 taxonomic ranks ] Bacteria phyloseq-class experiment-level object otu_table() OTU Table: [ 1186 taxa and 374 samples ] sample_data() Sample Data: [ 374 samples by 5 sample variables ] tax_table() Taxonomy Table: [ 1186 taxa by 7 taxonomic ranks ]

spholmes commented 3 years ago

Hi, I guess your first step is to "match samples" you need the same number of samples and they must match in name, then you could merge them: https://joey711.github.io/phyloseq/merge.html

best Susan

On Wed, May 26, 2021 at 1:03 AM KLequette @.***> wrote:

Hi,

I'm looking for study rhizosphere microbiote (fungi and bacteria) in R. I have two independent sequencing data (bacteria & fungi) and I would like to perform co-occurence analysis. I use phyloseq package but it is not clear if we can do this with phyloseq. Anyone did it ? If yes, how did you do ?

Cheers !

Fungi phyloseq-class experiment-level object otu_table() OTU Table: [ 214 taxa and 342 samples ] sample_data() Sample Data: [ 342 samples by 5 sample variables ] tax_table() Taxonomy Table: [ 214 taxa by 7 taxonomic ranks ] Bacteria phyloseq-class experiment-level object otu_table() OTU Table: [ 1186 taxa and 374 samples ] sample_data() Sample Data: [ 374 samples by 5 sample variables ] tax_table() Taxonomy Table: [ 1186 taxa by 7 taxonomic ranks ]

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