Track the number of reads (= sequences), samples and cluster (e.g. ASV) for each sample
Source:R/dada_phyloseq.R
track_wkflow_samples.Rd
Accept all input types supported by track_wkflow(): phyloseq objects,
matrices (samples x clusters), dada-class, derep-class, lists of
dada-class or derep-class, and character vectors of fastq/fastq.gz file
paths.
More information are available in the manual of the function track_wkflow()
Arguments
- list_of_objects
(required) a list of objects passed on to
track_wkflow(). Accepts phyloseq, matrix, dada-class, derep-class, lists of dada-class or derep-class, and character vectors of file paths.- output_data_frame
(logical, default FALSE) If TRUE, the function returns a data frame with the number of sequences, clusters and samples for each sample.
- ...
Other args passed on to
track_wkflow()
Value
A list of dataframe. cf track_wkflow() for more information
Examples
tree_A10_005 <- subset_samples(data_fungi, Tree_name == "A10-005")
if (requireNamespace("pbapply")) {
track_wkflow_samples(tree_A10_005)
}
#> You select 1 of 3 samples and conserved 67 out of 1420 taxa represented by 13314 sequences (out of 56868 sequences [23%])
#> Compute the number of sequences
#> Start object of class: phyloseq
#> Compute the number of clusters
#> Start object of class: phyloseq
#> Compute the number of samples
#> Start object of class: phyloseq
#> You select 1 of 3 samples and conserved 70 out of 1420 taxa represented by 39593 sequences (out of 56868 sequences [70%])
#> Compute the number of sequences
#> Start object of class: phyloseq
#> Compute the number of clusters
#> Start object of class: phyloseq
#> Compute the number of samples
#> Start object of class: phyloseq
#> You select 1 of 3 samples and conserved 54 out of 1420 taxa represented by 3961 sequences (out of 56868 sequences [7%])
#> Compute the number of sequences
#> Start object of class: phyloseq
#> Compute the number of clusters
#> Start object of class: phyloseq
#> Compute the number of samples
#> Start object of class: phyloseq
#> $`A10-005-B_S188_MERGED.fastq.gz`
#> nb_sequences nb_clusters nb_samples
#> 1 13314 67 1
#>
#> $`A10-005-H_S189_MERGED.fastq.gz`
#> nb_sequences nb_clusters nb_samples
#> 1 39593 70 1
#>
#> $`A10-005-M_S190_MERGED.fastq.gz`
#> nb_sequences nb_clusters nb_samples
#> 1 3961 54 1
#>