Filt_samples: Filt_samples function

In nearinj/Healthy_Oral_Microbiome: Analysis for Healthy Oral Microbiome Atlantic PATH Cohort

Description

This function takes a sequencing depth and whether you want to return the whole dataset, the completed cases dataset, or the dataset that was used for validation.

Usage

Filt_samples(
  depth = 5000,
  setType = "complete",
  Taxa_table,
  Metadata,
  cutoff_prop = 0.1,
  parallel = 1
)

Arguments

depth	The depth that you want to filter samples to. Defaults to 5000
setType	The dataset that type you want to return. Currently there are three options "complete" returns the completed cases dataset (main cohort), "validation" returns the validation cohort, "whole" returns all samples in the dataset.
Taxa_table	The ASV or genus table that is to be filtered.
Metadata	The metadata used for filtering.
cutoff_prop	The cutoff proportion for fitlering rare taxa.
parallel	The number of threads you want to use to filter your data.

Value

Returns both the filtered metadata and taxa_table in a list. Filtering is done as follows: Samples are filtered by read depth, rare taxa removed, and then samples filtered based on setType.

nearinj/Healthy_Oral_Microbiome documentation built on April 3, 2020, 12:58 a.m.