Open purinprima opened 5 years ago
Dear Joey,
I also want to know how to construct a phyleseq object from otu file, taxa and meta files.
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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-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/
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
sample1 1 1 sample2 2 1 etc