construct_phyloseq: Function to automatically generate a phyloseq object from...

In CMET-UGent/CMETNGS: Convenience functions for CMET NGS automated pipeline

Description

This function uses a shared file (i.e. a mothur-formatted OTU contingency table),a taxonomy file (i.e. an RDP naive bayesian fixed-rank asignment detail) and an optional fasta file with representative sequences for every OTU as well as an optional metadata file to be merged into a phyloseq object.

Usage

construct_phyloseq(
  shared,
  taxonomy,
  otureps = NULL,
  metadata = NULL,
  remove_singletons = TRUE,
  dataname = "phydata"
)

Arguments

shared	file location string for the shared file (preferably absolute path)
taxonomy	file location string for the taxonomy file (preferably absolute path)
otureps	optional file location for the respresentative fasta file ( preferably absolute path)
metadata	optional file location for the metadata.xlsx file (preferably absolute path)
remove_singletons	boolean (defaults to TRUE) indicating wether or not absolute singletonds should be removed
dataname	string indicating the name of data, will be used if the sample names are completely numerical as a prefix (default: "phydata")

Value

A phyloseq object

Examples

## Example without otureps
# make sure library(CMETNGS) is loaded

## Example with otureps

CMET-UGent/CMETNGS documentation built on Dec. 12, 2020, 8:22 a.m.