Designed with package integration in mind, the remove samples function allows you to remove samples from a strollur object
Arguments
- data,
a strollur object.
- samples,
vector of strings containing the names of the samples to remove.
- reason,
string containing the reason for removal. Default = "remove_samples".
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 = "sample")
#> [1] 19
# To remove samples 'F3D0' and 'F3D1'
xdev_remove_samples(data, c("F3D0", "F3D1"))
#> 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 2579.00
#> 25%-tile: 1 375 252 0 4 0 25781.00
#> Median: 1 375 252 0 4 0 51561.00
#> 75%-tile: 1 375 253 0 5 0 77341.00
#> 97.5%-tile: 1 375 253 0 6 0 100543.00
#> Maximum: 1 375 256 0 6 0 103120.00
#> Mean: 1 375 252 0 4 0 0.00
#> scrap_summary:
#> type trash_code unique total
#> 1 sequence remove_samples 204 215
#> 2 otu remove_samples 30 31
#> 3 asv remove_samples 204 215
#> 4 phylotype remove_samples 4 4
#>
#> Number of unique seqs: 2221
#> Total number of seqs: 103120
#>
#> Total number of samples: 17
#> Total number of treatments: 2
#> Total number of otus: 501
#> Total number of otu bin classifications: 501
#> Total number of asvs: 2221
#> Total number of asv bin classifications: 2221
#> Total number of phylotypes: 59
#> Total number of phylotype bin classifications: 59
#> Total number of sequence classifications: 2221
#> Total number of resource references: 2
#> Total number of custom reports: 1
#> Your dataset includes metadata
#>
count(data = data, type = "sample")
#> [1] 17