xdev_remove_lineages — xdev_remove

Designed with package integration in mind, the remove lineages function allows you to remove contaminents from a strollur

Usage

xdev_remove_lineages(data, contaminants, reason = "contaminant")

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

No return value, called for side effects.

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)