convert: Converters
In FelixErnst/mia: Microbiome analysis

convert

R Documentation

Converters

Description

For convenience, a few functions are available to convert BIOM, DADA2 and phyloseq objects to TreeSummarizedExperiment objects, and TreeSummarizedExperiment objects to phyloseq objects.

Usage

convertFromBIOM(
  x,
  prefix.rm = removeTaxaPrefixes,
  removeTaxaPrefixes = FALSE,
  rank.from.prefix = rankFromPrefix,
  rankFromPrefix = FALSE,
  artifact.rm = remove.artifacts,
  remove.artifacts = FALSE,
  ...
)

convertToBIOM(x, assay.type = "counts", ...)

## S4 method for signature 'SummarizedExperiment'
convertToBIOM(x, assay.type = "counts", ...)

convertFromDADA2(...)

convertFromPhyloseq(x)

convertToPhyloseq(x, ...)

## S4 method for signature 'SummarizedExperiment'
convertToPhyloseq(x, assay.type = "counts", assay_name = NULL, ...)

## S4 method for signature 'TreeSummarizedExperiment'
convertToPhyloseq(x, tree.name = tree_name, tree_name = "phylo", ...)

Arguments

`x`	a `TreeSummarizedExperiment` object
`prefix.rm`	`TRUE` or `FALSE`: Should taxonomic prefixes be removed? The prefixes is removed only from detected taxa columns meaning that `rank.from.prefix` should be enabled in the most cases. (default `prefix.rm = FALSE`)
`removeTaxaPrefixes`	Deprecated. Use `prefix.rm` instead.
`rank.from.prefix`	`TRUE` or `FALSE`: If file does not have taxonomic ranks on feature table, should they be scraped from prefixes? (default `rank.from.prefix = FALSE`)
`rankFromPrefix`	Deprecated.Use `rank.from.prefix` instead.
`artifact.rm`	`TRUE` or `FALSE`: If file have some taxonomic character naming artifacts, should they be removed. (default `artifact.rm = FALSE`)
`remove.artifacts`	Deprecated. Use `artifact.rm` instead.
`...`	Additional arguments. For `convertFromDADA2`, see `mergePairs` function for more details.
`assay.type`	A single character value for selecting the `assay` to be included in the phyloseq object that is created. (By default: `assay.type = "counts"`)
`assay_name`	a single `character` value for specifying which assay to use for calculation. (Please use `assay.type` instead. At some point `assay_name` will be disabled.)
`tree.name`	a single `character` value for specifying which tree will be included in the phyloseq object that is created, (By default: `tree.name = "phylo"`)
`tree_name`	Deprecated. Use `tree.name` instead.

Details

convertFromBIOM coerces a BIOM object to a TreeSummarizedExperiment object.

convertFromBIOM coerces a TreeSummarizedExperiment object to a biom object.

convertFromDADA2 is a wrapper for the mergePairs function from the dada2 package. A count matrix is constructed via makeSequenceTable(mergePairs(...)) and rownames are dynamically created as ASV(N) with N from 1 to nrow of the count tables. The colnames and rownames from the output of makeSequenceTable are stored as colnames and in the referenceSeq slot of the TreeSummarizedExperiment, respectively.

convertFromPhyloseq converts phyloseq objects into TreeSummarizedExperiment objects. All data stored in a phyloseq object is transferred.

convertToPhyloseq creates a phyloseq object from a TreeSummarizedExperiment object. By using assay.type, it is possible to specify which table from assay is added to the phyloseq object.

Value

convertFromBIOM returns an object of class TreeSummarizedExperiment

convertFromDADA2 returns an object of class TreeSummarizedExperiment

convertFromPhyloseq returns an object of class TreeSummarizedExperiment

convertToPhyloseq returns an object of class phyloseq

Author(s)

Leo Lahti and Tuomas Borman. Contact: microbiome.github.io

Examples


# Convert BIOM results to a TreeSE
# Load biom file
library(biomformat)
biom_file <- system.file("extdata", "rich_dense_otu_table.biom",
                         package = "biomformat")

# Make TreeSE from BIOM object
biom_object <- biomformat::read_biom(biom_file)
tse <- convertFromBIOM(biom_object)

# Convert TreeSE object to BIOM
biom <- convertToBIOM(tse)


### Coerce DADA2 results to a TreeSE object
if(requireNamespace("dada2")) {
  fnF <- system.file("extdata", "sam1F.fastq.gz", package="dada2")
  fnR = system.file("extdata", "sam1R.fastq.gz", package="dada2")
  dadaF <- dada2::dada(fnF, selfConsist=TRUE)
  dadaR <- dada2::dada(fnR, selfConsist=TRUE)

  tse <- convertFromDADA2(dadaF, fnF, dadaR, fnR)
  tse
}

### Coerce a phyloseq object to a TreeSE object
if (requireNamespace("phyloseq")) {
    data(GlobalPatterns, package="phyloseq")
    convertFromPhyloseq(GlobalPatterns)
    data(enterotype, package="phyloseq")
    convertFromPhyloseq(enterotype)
    data(esophagus, package="phyloseq")
    convertFromPhyloseq(esophagus)
}

### Coerce a TreeSE object to a phyloseq object
# Get tse object
data(GlobalPatterns)
tse <- GlobalPatterns

# Create a phyloseq object from it
phy <- convertToPhyloseq(tse)
phy

# By default the chosen table is counts, but if there are other tables,
# they can be chosen with assay.type.

# Counts relative abundances table
tse <- transformAssay(tse, method = "relabundance")
phy2 <- convertToPhyloseq(tse, assay.type = "relabundance")
phy2

FelixErnst/mia documentation built on July 15, 2024, 9:21 p.m.