transformcounts: Transform abundance data in an 'otu_table', sample-by-sample.

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

Transform abundance data in an otu_table, sample-by-sample.

Description

This function transforms the sample counts of a taxa abundance matrix according to a user-provided function. The counts of each sample will be transformed individually. No sample-sample interaction/comparison is possible by this method.

Usage

transform_sample_counts(physeq, fun, ...)

transformSampleCounts(physeq, fun, ...)

Arguments

physeq	(Required). phyloseq-class of otu_table-class.
fun	(Required). A single-argument function that will be applied to the abundance counts of each sample. Can be an anonymous function.
...	(Optional). Additional, optionally-named, arguments passed to fun during transformation of abundance data.

Value

A transformed otu_table – or phyloseq object with its transformed otu_table. In general, trimming is not expected by this method, so it is suggested that the user provide only functions that return a full-length vector. Filtering/trimming can follow, for which the genefilter_sample and prune_taxa functions are suggested.

See Also

threshrankfun, rank, log

Examples

#
data(esophagus)
x1 = transform_sample_counts(esophagus, threshrankfun(50))
head(otu_table(x1), 10)
x2 = transform_sample_counts(esophagus, rank)
head(otu_table(x2), 10)
identical(x1, x2)
x3 = otu_table(esophagus) + 5
x3 = transform_sample_counts(x3, log)
head(otu_table(x3), 10)
x4 = transform_sample_counts(esophagus, function(x) round(x^2.2, 0))
head(otu_table(x4), 10)

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.