clr.transform: Center Log Ratio tranform phyloseq

In kstagaman/phyloseqCompanion: Provides additional functions to work with phyloseq objects

Center Log Ratio tranform phyloseq

Description

CLR transform abundance counts in the otu_matrix of a phyloseq object and return whole phyloseq object.

Usage

clr.transform(
  ps,
  min_reads = NULL,
  min_prop = 0.001,
  min_occur = 0,
  smpls_by_row = TRUE,
  method = "CZM",
  lab = 0
)

Arguments

ps	a phyloseq object.
min_reads	The minimum reads per sample. Default=min(sample_sums(ps))
min_prop	The minimum proportional abundance of a read in any sample. Default=0.001.
min_occur	The minimum fraction of non-0 reads for each variable in all samples. Default=0
smpls_by_row	True if rows contain samples, false if rows contain variables. Default=TRUE
method	Geometric Bayesian multiplicative (GBM, default); square root BM (SQ); Bayes-Laplace BM (BL); count zero multiplicative (CZM); user-specified hyper-parameters (user). Default="CZM"
lab	Unique label (numeric or character) used to denote count zeros in X (default label=0).

See Also

phyloseq, codaSeq.filter, cmultRepl, codaSeq.clr

Examples

data(example_phyloseq)

clr.ps <- clr.transform(example_phyloseq, min_reads = 10000)

kstagaman/phyloseqCompanion documentation built on Aug. 26, 2022, 5:07 a.m.