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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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Combining otu, taxa and meta files into phyloseq object #1183

Open purinprima opened 5 years ago

purinprima commented 5 years ago

Hi Joey,

I have separate otu, taxa and meta files in txt and would like to combine those three files into a phyloseq object. Could you please suggest R scripts to combine those 3 files? Many thanks in advance.

The arrangement of each file is as follow:

otu file

OTU.ID sample1 sample2 etc OTU_1 0.0028 0.0571 OTU_2 0.0041 0.0548 OTU_3 0.0275 0.0834 etc

taxa file

kingdom phylum class order family genus species kBacteria pProteobacteria cAlphaproteobacteria oSphingomonadales fSphingomonadaceae gSphingobium s kBacteria pPatescibacteria cSaccharimonadia oSaccharimonadales f g s

meta file

                    treatment           replicate        etc

sample1 1 1 sample2 2 1 etc

JunqiangZheng commented 5 years ago

Dear Joey,

I also want to know how to construct a phyleseq object from otu file, taxa and meta files.

spholmes commented 5 years ago

Please follow the tutorial here: https://joey711.github.io/phyloseq/import-data.html

a good idea is to follow it with the example data and then try your own data after you understand how it works on perfectly formatted data first, Best of luck, Susan

On Sun, Jul 7, 2019 at 2:43 AM JunqiangZheng notifications@github.com wrote:

Dear Joey,

I also want to know how to construct a phyleseq object from otu file, taxa and meta files.

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