Designed with package integration in mind, the remove bins function allows you to remove bins from a strollur object
Arguments
- data,
a strollur object.
- bin_names,
a vector of strings containing the names of the bins you would like removed.
a vector of strings containing the reasons you are removing each bin
- bin_type
a string indicating the type of clusters.
Value
an updated strollur object
Examples
data <- new_dataset(dataset_name = "my_dataset")
bin_names <- c("bin1", "bin2", "bin3")
abundances <- c(110, 525, 80)
xdev_assign_bins(data = data,
table = data.frame(bin_name = bin_names,
abundance = abundances),
bin_type = "otu")
#> Assigned 3 otu bins.
#> my_dataset:
#>
#>
#> Number of unique seqs: 3
#> Total number of seqs: 715
#>
#> Total number of otus: 3
#>
count(data = data, type = "bin", bin_type = "otu")
#> [1] 3
bins_to_remove <- c("bin1")
trash_tag <- c("bad_bin")
xdev_remove_bins(data = data,
bin_names = bins_to_remove,
trash_tags = trash_tag)
#> my_dataset:
#>
#> scrap_summary:
#> type trash_code unique total
#> 1 sequence bad_bin 1 110
#> 2 otu bad_bin 1 110
#>
#> Number of unique seqs: 2
#> Total number of seqs: 605
#>
#> Total number of otus: 2
#>
count(data = data, type = "bin", bin_type = "otu")
#> [1] 2