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,
  ...
)

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
...	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()

Examples

data(enterotype)
if (requireNamespace("pbapply")) {
  track_wkflow(list(data_fungi, enterotype), taxonomy_rank = c(3, 5))
}

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.