xdev_merge_bins

Designed with package integration in mind, the merge bins function allows you to merge bins in a strollur object

Usage

xdev_merge_bins(data, bin_names, reason = "merged", bin_type = "otu")

Arguments

data,

a strollur object.

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

No return value, called for side effects.

Examples

 data <- 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 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added metadata.
#> Added 2 resource references.
#> Added a contigs_report.

 # to merge otu5 and otu6

 bins_to_merge <- c("Otu005", "Otu006")

 xdev_merge_bins(data = data, bin_names = bins_to_merge)

 # If you look at the scrap report, you will see Otu006 with the trash code
 # set to "merged".

 report(data = data, type = "bin_scrap")
#>       id trash_code
#> 1 Otu006     merged