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Track the number of reads (= sequences), samples and cluster (e.g. ASV) from various objects including dada-class and derep-class.

Source: R/dada_phyloseq.R
track_wkflow.Rd

lifecycle-maturing

  • List of fastq and fastg.gz files -> nb of reads and samples

  • List of dada-class -> nb of reads, clusters (ASV) and samples

  • List of derep-class -> nb of reads, clusters (unique sequences) and samples

  • Matrix of samples x clusters (e.g. otu_table) -> nb of reads, clusters and samples

  • Phyloseq-class -> nb of reads, clusters and samples

Usage

track_wkflow(
  list_of_objects,
  obj_names = NULL,
  clean_pq = FALSE,
  taxonomy_rank = NULL,
  verbose = TRUE,
  ...
)

Arguments

list_of_objects

(required) a list of objects

obj_names

A list of names corresponding to the list of objects

clean_pq

(logical) If set to TRUE, empty samples and empty ASV are discarded before clustering.

taxonomy_rank

A vector of int. Define the column number of taxonomic rank in physeq@tax_table to compute the number of unique value. Default is NULL and do not compute values for any taxonomic rank

verbose

(logical) If true, print some additional messages.

...

Other arguments passed on to clean_pq() function.

Value

The number of sequences, clusters (e.g. OTUs, ASVs) and samples for each object.

See also

track_wkflow_samples()

Author

Adrien Taudière

Examples

data(enterotype)
if (requireNamespace("pbapply")) {
  track_wkflow(list(data_fungi, enterotype), taxonomy_rank = c(3, 5))
  track_wkflow(list(
    "data FUNGI" = data_fungi,
    "fastq files forward" =
      unlist(list_fastq_files(system.file("extdata", package = "MiscMetabar"),
        paired_end = FALSE
      ))
  ))
}
#> Compute the number of sequences
#> Start object of class: phyloseq
#> Start object of class: phyloseq
#> Compute the number of clusters
#> Start object of class: phyloseq
#> Start object of class: phyloseq
#> Compute the number of samples
#> Start object of class: phyloseq
#> Start object of class: phyloseq
#> Compute the number of values in taxonomic rank
#> Start object of class: phyloseq
#> Start object of class: phyloseq
#> Start object of class: phyloseq
#> Start object of class: phyloseq
#> Compute the number of sequences
#> Start object of class: phyloseq
#> Start object of class: character
#> Compute the number of clusters
#> Start object of class: phyloseq
#> Start object of class: character
#> Compute the number of samples
#> Start object of class: phyloseq
#> Start object of class: character
#>                     nb_sequences nb_clusters nb_samples
#> data FUNGI               1839124        1420        185
#> fastq files forward          100          NA          1