Designed with package integration in mind, the merge bins function allows you to merge bins in a strollur object
Arguments
- data
- bin_names
a vector of strings containing the names of the bins you would like merge. The resulting merged bin will be stored in the first bin_id in the vector.
- reason
a string indicating why you are merging bins. Default = "merged".
- bin_type
a string indicating the type of bin clusters. Default = "otu"
Value
an updated strollur object
Examples
data <- strollur::miseq_sop_example()
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 2425 asv bins.
#> Assigned 63 phylotype bins.
#> Assigned 19 samples to treatments.
#> Assigned 171 samples distances.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added a metadata report.
#> Added 2 resource references.
#> Added a contigs_report report.
# to merge otu5 and otu6
bins_to_merge <- c("Otu005", "Otu006")
strollur::xdev_merge_bins(data,
bin_names = bins_to_merge)
#> miseq_sop:
#>
#> starts ends nbases ambigs polymers numns numseqs
#> Minimum: 1 375 249 0 3 0 1.00
#> 2.5%-tile: 1 375 252 0 4 0 2850.05
#> 25%-tile: 1 375 252 0 4 0 28491.50
#> Median: 1 375 253 0 4 0 56982.00
#> 75%-tile: 1 375 253 0 5 0 85472.50
#> 97.5%-tile: 1 375 254 0 6 0 111113.95
#> Maximum: 1 375 256 0 6 0 113963.00
#> Mean: 1 375 252 0 4 0 56982.00
#>
#> scrap_summary:
#> type trash_code unique total
#> 1 otu merged 1 6621
#>
#> Number of unique seqs: 2425
#> Total number of seqs: 113963
#>
#> Total number of samples: 19
#> Total number of treatments: 2
#> Total number of otus: 530
#> Total number of otu bin classifications: 530
#> Total number of asvs: 2425
#> Total number of asv bin classifications: 2425
#> Total number of phylotypes: 63
#> Total number of phylotype bin classifications: 63
#> Total number of sequence classifications: 2425
#> Total number of resource references: 2
#> Total number of custom reports: 2
#>
# If you look at the scrap report, you will see Otu006 with the trash code
# set to "merged".
strollur::report(data, type = "bin_scrap")
#> bin_name trash_code
#> 1 Otu006 merged