In microsud/chkMocks: Compare Mock Community Samples in Microbiome Sequencing Studies

library(chkMocks)
library(phyloseq)

ps <- readRDS("../data-raw/Karstens2019.rds")
ps
# check taxa names are ASVs
#taxa_names(ps)[1:2] 

ps <-  subset_samples(ps,sample_names(ps)!= 'Blank')
ZymoExamplePseq <- prune_taxa(taxa_sums(ps)>0,ps)
#table(tax_table(ps)[,"Genus"], useNA = "always")
sample_sums(ZymoExamplePseq)

usethis::use_data(ZymoExamplePseq, overwrite = TRUE, compress = "xz")

microsud/chkMocks documentation built on July 1, 2023, 9:23 p.m.