Compare ZymoBiomics to Experimental

checkZymoBiomics(
  x,
  mock_db = NULL,
  multithread = 2,
  threshold = 60,
  verbose = FALSE,
  strand = "top",
  ...
)

Arguments

x: Phyloseq objects where taxa_names are ASV sequences
mock_db: ZymoTrainingSet
multithread: Passed on to DECIPHER::IdTaxa Default is NULL
threshold: Passed on to DECIPHER::IdTaxa. Default is 60
verbose: Default is FALSE
strand: DECIPHER::IdTaxa Default is top
...: Arguments to pass on to DECIPHER::IdTaxa

Value

List with pseq, and cor table

Details

Compare ZymoBiomics theoretical to Experimental composition.

Author

Sudarshan Shetty sudarshanshetty9@gmail.com

Examples

library(phyloseq)

output.dat <- checkZymoBiomics(ZymoExamplePseq,
                               mock_db = ZymoTrainingSet,
                               multithread= 2,
                               threshold = 80,
                               strand = "top",
                               verbose = FALSE)
#> Using internal reference database
#>             for ZymoBiomics
#> Warning: Expected 8 pieces. Missing pieces filled with `NA` in 937 rows [9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, ...].