transform: Data Transformations for phyloseq Objects

In microbiome/microbiome: Microbiome Analytics

Data Transformations for phyloseq Objects

Description

Standard transforms for phyloseq-class.

Usage

transform(
  x,
  transform = "identity",
  target = "OTU",
  shift = 0,
  scale = 1,
  log10 = TRUE,
  reference = 1,
  ...
)

Arguments

x	phyloseq-class object
transform	Transformation to apply. The options include: 'compositional' (ie relative abundance), 'Z', 'log10', 'log10p', 'hellinger', 'identity', 'clr', 'alr', 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".
log10	Used only for Z transformation. Apply log10 before Z.
reference	Reference feature for the alr transformation.
...	arguments to be passed

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
# Note that small pseudocount is added if data contains zeroes
xt <- microbiome::transform(x, 'clr')

# ALR transform
# The pseudocount must be specified explicitly
# The reference feature is 1 by default
xt <- microbiome::transform(x, 'alr', shift=1, reference=1)

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

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

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.