load_data: Load ABRP 16S data and filter out low abundance taxa

In kimberlyroche/ROL: What the package does (short line)

Description

Load ABRP 16S data and filter out low abundance taxa

Usage

load_data(
  tax_level = "ASV",
  host_sample_min = 75,
  count_threshold = 5,
  sample_threshold = 0.2
)

Arguments

tax_level	taxonomic level at which to agglomerate data
host_sample_min	minimum sample number for host inclusion in the filtered data set
count_threshold	minimum count at which a taxon must be observed
sample_threshold	minimum proportion of samples within each host at which a taxon must be observed at the level specified by count_threshold

Details

Together count_threshold and sample_threshold specify a minimum representation for a taxon. Taxa below these observed thresholds will be grouped together into a category "Other."

Value

phyloseq object

Examples

data <- load_data(tax_level="ASV", host_sample_min=75, count_threshold=5, sample_threshold=0.2)

kimberlyroche/ROL documentation built on Dec. 10, 2020, 2:18 a.m.