transform: Data Transformations for phyloseq Objects

In microbiome: Microbiome Analytics

Description

Standard transforms for phyloseq-class.

Usage

transform(x, transform = "identity", target = "OTU", shift = 0, scale = 1)

Arguments

x	phyloseq-class object
transform	Transformation to apply. The options include: 'compositional' (ie relative abundance), 'Z', 'log10', 'log10p', 'hellinger', 'identity', 'clr', or any method from the vegan::decostand function.
target	Apply the transform for 'sample' or 'OTU'. Does not affect the log transform.
shift	A constant indicating how much to shift the baseline abundance (in transform='shift')
scale	Scaling constant for the abundance values when transform = "scale".

Details

In transformation typ, the 'compositional' abundances are returned as relative abundances in [0, 1] (convert to percentages by multiplying with a factor of 100). The Hellinger transform is square root of the relative abundance but instead given at the scale [0,1]. The log10p transformation refers to log10(1 + x). The log10 transformation is applied as log10(1 + x) if the data contains zeroes. CLR transform applies a pseudocount of min(relative abundance)/2 to exact zero relative abundance entries in OTU table before taking logs.

Value

Transformed phyloseq object

Examples

data(dietswap)
x <- dietswap

# No transformation
xt <- transform(x, 'identity')

# OTU relative abundances
# xt <- transform(x, 'compositional')

# Z-transform for OTUs
# xt <- transform(x, 'Z', 'OTU')

# Z-transform for samples
# xt <- transform(x, 'Z', 'sample')

# Log10 transform (log10(1+x) if the data contains zeroes)
# xt <- transform(x, 'log10')

# Log10p transform (log10(1+x) always)
# xt <- transform(x, 'log10p')

# CLR transform
xt <- microbiome::transform(x, 'clr')

# Shift the baseline
# xt <- transform(x, 'shift', shift=1)

# Scale
# xt <- transform(x, 'scale', scale=1)

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.