track_wkflow: Track the number of reads (= sequences), samples and cluster...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

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

Description

• 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.

Author(s)

Adrien Taudière

See Also

track_wkflow_samples()

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
      ))
  ))
}

adrientaudiere/MiscMetabar documentation built on Dec. 19, 2024, 3:16 a.m.