Subsample.Table: Subsample.Table

In jbisanz/MicrobeR: Handy functions for microbiome analysis in R

Description

Takes a Feature/OTU/SV table where samples are columns and feature names are row names. This was formerly using the VEGAN rrarefy function but was found to be slow on large numbers of samples (~3000). Suspected this was due to serial/vectorized implimentations. Now this function is really just an alias for rarefy_even_depth from phyloseq. NOTE: Sampling with replacement!

Usage

Subsample.Table(FEATURES, DEPTH, SEED, VERBOSE)

Arguments

DEPTH	Count depth, defaults to min(colSums(OTUTABLE)) if not passed
SEED	A randomization SEED, defaults to 182.
VERBOSE	Should progress and metrics be printed to screen via message()? Default=TRUE
OTUTABLE	Table of feature/OTU/SV counts where Samples are columns, and IDs are row names

Value

Subsampled Table

jbisanz/MicrobeR documentation built on June 5, 2019, 7:53 p.m.