Filtering phyloseq object by sample ids

I have a phyloseq object and I would like to filter by sample ids read from a text file.

How can I do that?

r phyloseq filtering microbiome

• 2,823 views • link

written 10.7 years ago by nadne •

0 answers

No answers yet.

More posts like this

Phyloseq sample data error: non-zero dimensions?
written 2.8 years ago by Emily •

I'm trying to filter/extract out individuals from the genetic data that has a gut gene data. Got an `Error` message saying that my Phyloseq object …
How to add a refseq() slot to a MAG based phyloseq object ?
written 3.1 years ago by v.berriosfarias •

Hello, I was asked to build a phyloseq object from some metagenome assembled genomes that I built. By far I have created a tax_table() slot …
How to remove duplicate reads after ONT basecalling from fastq.gz files
written 3.4 years ago by Darrenjdd •

Hi I ran into an error when my PC was halfway through basecalling, it errored on a fast5 file - number 577. I restarted basecalling …
OTU Table Extraction from Phyloseq Object
written 4.2 years ago by safiq713 •

I want to extract otu table from the phyloseq object: > physeq_N phyloseq-class experiment-level object otu_table() OTU Table: [ 1581 taxa and 4 samples ] …
Issues removing unwanted taxa from phyloseq object
written 4.4 years ago by bioinfo_or_bust •

Hi everyone, I am currently in the process of removing unwanted taxa (Kingdom="Eukaryota", Family="Mitochondria", and Order="Chloroplast") from a phyloseq object I created. This phyloseq object …
How to filter a gff3 file by gene IDs
written 5.6 years ago by William

How to filter a gff3 file by gene IDs? Just grepping on the IDs does output the exons and other features that are below the …
meta file table
written 6.6 years ago by figueroacg •

Hi, How can I generate a meta file table from a list of text files? I have a text file with multiple file names, like …
How to split BAM files by samples from PacBio
written 7.7 years ago by misterie

Hi, I have sequences from 6 bacterias (E. Coli and Salmonella). 6 samples have been sequenced using PacBio on 4 movies so I have 3 …
How to fix Error in `$<-.data.frame`(`*tmp*`, "Kingdom", value = character(0)) : replacement has …
written 8.0 years ago by arsilan324

Hi all, I am stuck with this error. Error in `$<-.data.frame`(`*tmp*`, "Kingdom", value = character(0)) : replacement has 0 rows, data has 2407 This is …
Mapping old Ensembl transcript to a newer one
written 11.1 years ago by nadne •

I have a bunch of human Ensembl transcript ids from an old release, that I want to find the ids in the current version. For …