Designed with package integration in mind, the remove sequences function allows you to remove sequences from a strollur object
Arguments
- data,
a strollur object.
- sequence_names,
vector of strings containing the names of the sequences to remove
vector of strings containing the reasons for the sequences removals
Value
an updated strollur object
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.
count(data = data, type = "sequence")
#> [1] 113963
# For the sake of example let's remove the first 3 sequences from
# miseq_sop_example:
seqs_to_remove <- c("M00967_43_000000000-A3JHG_1_2101_16474_12783",
"M00967_43_000000000-A3JHG_1_1113_12711_3318",
"M00967_43_000000000-A3JHG_1_2108_14707_9807")
trash_codes <- c("example", "removing", "sequences")
xdev_remove_sequences(data = data, sequence_names = seqs_to_remove,
trash_tags = trash_codes)
#> 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 3 0 2850.00
#> 25%-tile: 1 375 252 0 4 0 28491.00
#> Median: 1 375 252 0 4 0 56981.00
#> 75%-tile: 1 375 253 0 5 0 85471.00
#> 97.5%-tile: 1 375 253 0 6 0 111112.00
#> Maximum: 1 375 256 0 6 0 113960.00
#> Mean: 1 375 252 0 4 0 0.00
#> scrap_summary:
#> type trash_code unique total
#> 1 sequence example 1 1
#> 2 sequence removing 1 1
#> 3 sequence sequences 1 1
#> 4 asv example 1 1
#> 5 asv removing 1 1
#> 6 asv sequences 1 1
#>
#> Number of unique seqs: 2422
#> Total number of seqs: 113960
#>
#> Total number of samples: 19
#> Total number of treatments: 2
#> Total number of otus: 531
#> Total number of otu bin classifications: 531
#> Total number of asvs: 2422
#> Total number of asv bin classifications: 2422
#> Total number of phylotypes: 63
#> Total number of phylotype bin classifications: 63
#> Total number of sequence classifications: 2422
#> Total number of resource references: 2
#> Total number of custom reports: 1
#> Your dataset includes metadata
#>
# If you look at the scrap report, you the sequences names, listed with the
# trash codes set to "example", "removing", "sequences".
report(data = data, type = "sequence_scrap")
#> id trash_code
#> 1 M00967_43_000000000-A3JHG_1_2101_16474_12783 example
#> 2 M00967_43_000000000-A3JHG_1_1113_12711_3318 removing
#> 3 M00967_43_000000000-A3JHG_1_2108_14707_9807 sequences
# You can see from the get_num_sequences function that the removed
# sequence's abundances are removed from the dataset.
count(data = data, type = "sequence")
#> [1] 113960