Designed with package integration in mind, the remove lineages function allows you to remove contaminents from a strollur
Arguments
- data,
a strollur object.
- contaminants,
vector of strings containing the taxonomies you would like to remove
- reason,
a string containing reason you are removing the lineages. Default = "contaminant".
Value
an updated strollur object
Examples
data <- read_mothur(fasta = strollur_example("final.fasta.gz"),
count = strollur_example("final.count_table.gz"),
taxonomy = strollur_example("final.taxonomy.gz"),
design = strollur_example("mouse.time.design"),
otu_list = strollur_example("final.opti_mcc.list.gz"),
dataset_name = "miseq_sop")
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 19 samples to treatments.
contaminants <- c("Chloroplast", "Mitochondria", "unknown", "Archaea",
"Eukaryota")
xdev_remove_lineages(data = data, contaminants = contaminants)
#> 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 2850.08
#> 25%-tile: 1 375 252 0 4 0 28491.75
#> Median: 1 375 252 0 4 0 56982.50
#> 75%-tile: 1 375 253 0 5 0 85473.25
#> 97.5%-tile: 1 375 253 0 6 0 111114.93
#> Maximum: 1 375 256 0 6 0 113963.00
#> Mean: 1 375 252 0 4 0 0.00
#>
#> Number of unique seqs: 2425
#> Total number of seqs: 113963
#>
#> 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 sequence classifications: 2425
#>