Hi,
I am trying to do network analysis from amplicon sequencing data. My aim is to identify hub species in the network. I am using the below code but spiec.easi step is taking lots of time. Is there any other way to speed up this or can we use any other alternative?
I will be thankful for your time and help.
#For testing reduce the number of ASVs
ps1.stool.otu <- prune_taxa(taxa_sums(ps1.stool) > 100, ps1.stool)
# Add taxonomic classification to OTU ID
ps1.stool.otu.f <- microbiomeutilities::format_to_besthit(ps1.stool.otu)
## Warning: replacing previous import 'ggplot2::alpha' by 'microbiome::alpha' when
## loading 'microbiomeutilities'
head(tax_table(ps1.stool.otu))
otu.c <- t(otu_table(ps1.stool.otu.f)@.Data) #extract the otu table from phyloseq object
tax.c <- as.data.frame(tax_table(ps1.stool.otu.f)@.Data)#extract the taxonomy information
head(tax.c)
# In practice, use more repetitions
set.seed(1244)
net.c <- spiec.easi(otu.c, method='mb', icov.select.params=list(rep.num=50)) # reps have to increases for real data
Many thanks