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jbisanz / qiime2R

Import qiime2 artifacts to R
MIT License
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Phyloseq object not recognizing negative control #40

Closed Avtober closed 2 years ago

Avtober commented 3 years ago

Hi there

When I try to make a phyloseq object with the following code, the phyloseq object seems to only recognise the samples not the negative controls. Does anyone know why this may be happening? I have the names of the controls in my metadata file so they should be coming up.

library("qiime2R") physeq3<-qza_to_phyloseq( features="DADA2-table4andneg.qza", tree="rooted-tree4andneg.qza", "NCBI_LSURef_97_10_uniq_5-8-300_classification_VSEARCHwithneg.qza", metadata = "metadata-2.txt") physeq3

Thanks

Avtober commented 3 years ago

Hi, just to add to this when I import the files separately using read_qza I can see the negative is in there but it is just when I use the qza_to_phyloseq that it does not seem to recognize it as a sample. Is there a way to just read the files in using read_qza then combining these files into a phyloseq object?

Thanks A

jbisanz commented 2 years ago

Do the negative controls have reads assigned to them? I wonder if phyloseq is stripping them out.