Using phyloseq structure for different data types?

[mirpie]

Hi there!

So this is a bit of an unconventional question, but I have some brain volume data on my hands and was wondering if I could co-opt some of phyloseq's very convenient functionality for this non-microbiome dataset. I have similar components to those used for construction of a regular phyloseq object, including a "taxonomy table" that classifies each brain sub-region based on the larger structure it belongs to. Is this a possibility, and as long as I ensure unique brain region ID's (analogous to OTU #s) align across tables?

Thanks!

[spholmes]

Hi There are other Bioconductor list types that are probably better for this : Have you looked at SummarizedExperiment or TreeSummarizedExperiment https://bioconductor.org/packages/release/bioc/html/TreeSummarizedExperiment.html ?

On Thu, Jan 20, 2022 at 2:06 PM mirpie @.***> wrote:

Hi there!

So this is a bit of an unconventional question, but I have some brain volume data on my hands and was wondering if I could co-opt some of phyloseq's very convenient functionality for this non-microbiome dataset. I have similar components to those used for construction of a regular phyloseq object, including a "taxonomy table" that classifies each brain sub-region based on the larger structure it belongs to. Is this a possibility, and as long as I ensure unique brain region ID's (analogous to OTU #s) align across tables?

Thanks!

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-- Susan Holmes

[mirpie]

Hi! These seem like exactly what I'm looking for, thanks! Any advice on constructing a tree for this data type? I've got both the data.frame and the data.tree available to me, but I can't find a way to make those compatible or convert them to a phylo/rpart object.

Thanks so much again!

Miranda

On Thu, Jan 20, 2022 at 7:06 PM Susan Holmes @.***> wrote:

Hi There are other Bioconductor list types that are probably better for this : Have you looked at SummarizedExperiment or TreeSummarizedExperiment

https://bioconductor.org/packages/release/bioc/html/TreeSummarizedExperiment.html ?

On Thu, Jan 20, 2022 at 2:06 PM mirpie @.***> wrote:

Hi there!

So this is a bit of an unconventional question, but I have some brain volume data on my hands and was wondering if I could co-opt some of phyloseq's very convenient functionality for this non-microbiome dataset. I have similar components to those used for construction of a regular phyloseq object, including a "taxonomy table" that classifies each brain sub-region based on the larger structure it belongs to. Is this a possibility, and as long as I ensure unique brain region ID's (analogous to OTU #s) align across tables?

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/joey711/phyloseq/issues/1545, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAJFZPNWWD7OCXOFIHZFJBTUXCBOFANCNFSM5MN5XQRQ

. Triage notifications on the go with GitHub Mobile for iOS < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675

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