benjjneb
commented
2 years ago On (1), You would use the same command to remove the taxa idenfied as contaminants, whatever methods you are using. All of them create a TRUE/FALSE vector in the $contaminant column of the returned data.frame that indicates the classified contaminants.
On (2), just set isContaminant(..., method="combined"). You'll also need to provide both the conc and neg arguments to the function as well (see the argument descriptions in ?isContaminant).
K-Gutierrez
Hi, this is an excellent program for checking contamination in amplicon sequencing samples. I am new in R, so I am following this tutorial: https://benjjneb.github.io/decontam/vignettes/decontam_intro.html#putting-it-all-together
I have two questions:
1) How can I remove the contaminants using the prevalence option, I am looking for a similar command such as you wrote in the Frequency section:
$ps
phyloseq-class experiment-level object
otu_table() OTU Table: [ 1951 taxa and 569 samples ]
sample_data() Sample Data: [ 569 samples by 6 sample variables ]
tax_table() Taxonomy Table: [ 1951 taxa by 6 taxonomic ranks ]
$ps.noncontam <- prune_taxa(!contamdf.freq$contaminant, ps) ps.noncontam
phyloseq-class experiment-level object
otu_table() OTU Table: [ 1893 taxa and 569 samples ]
sample_data() Sample Data: [ 569 samples by 6 sample variables ]
tax_table() Taxonomy Table: [ 1893 taxa by 6 taxonomic ranks ]
2) I would like to use the combined method. What is the command that I need to run?
Thanks in advance.