zscore: Z-score normalize relative abundance data

In OTUtable: North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions

Description

Normalizes taxa abundances in a table of relative abundance data using the z-score method. ((Abundance of one OTU in one sample) - (mean abundance for that OTU ))/(standard deviation of that OTU)

Usage

zscore(table)

Arguments

table

A table of relative abundance data with taxa in rows and samples in columns

Value

Returns a table with relative abundance data replaced by z-scores

Note

There is debate on whether this method of normalization is valid for microbial communities, as their abundance distrubtions tend to be heavily skewed. I found it useful for plotting heatmaps and for input into network analysis.

Author(s)

Alexandra Linz <[e-mail]>

Examples

data(otu_table)

# Create a small table for z-score normalization
example <- year_subset("05", otu_table)
example <- bog_subset("TBE", example)

# Remove OTUs that are not present in this subset
example <- example[which(rowSums(example) > 0), ]

z_otu_table <- zscore(example)

Example output

OTUtable documentation built on May 1, 2019, 10:51 p.m.