importQIIME2: Import QIIME2 results to 'TreeSummarizedExperiment'
In FelixErnst/mia: Microbiome analysis

importQIIME2

R Documentation

Import QIIME2 results to `TreeSummarizedExperiment`

Description

Results exported from QIMME2 can be imported as a TreeSummarizedExperiment using importQIIME2. Except for the assay.file, the other data types, row.file, refseq.file and tree.file, are optional, but are highly encouraged to be provided.

Import the QIIME2 artifacts to R.

Usage

importQIIME2(
  assay.file = featureTableFile,
  featureTableFile,
  row.file = taxonomyTableFile,
  taxonomyTableFile = NULL,
  col.file = sampleMetaFile,
  sampleMetaFile = NULL,
  as.refseq = featureNamesAsRefSeq,
  featureNamesAsRefSeq = TRUE,
  refseq.file = refSeqFile,
  refSeqFile = NULL,
  tree.file = phyTreeFile,
  phyTreeFile = NULL,
  ...
)

importQZA(file, temp.dir = temp, temp = tempdir(), ...)

Arguments

`assay.file`	a single `character` value defining the file path of the feature table to be imported.
`featureTableFile`	Deprecated. use `assay.file` instead.
`row.file`	a single `character` value defining the file path of the taxonomy table to be imported. (default: `row.file = NULL`).
`taxonomyTableFile`	Deprecated. use `row.file` instead.
`col.file`	a single `character` value defining the file path of the sample metadata to be imported. The file has to be in tsv format. (default: `col.file = NULL`).
`sampleMetaFile`	Deprecated. Use `col.file` instead.
`as.refseq`	`TRUE` or `FALSE`: Should the feature names of the feature table be regarded as reference sequences? This setting will be disregarded, if `refseq.file` is not `NULL`. If the feature names do not contain valid DNA characters only, the reference sequences will not be set.
`featureNamesAsRefSeq`	Deprecated. Use `as.refseq` instead.
`refseq.file`	a single `character` value defining the file path of the reference sequences for each feature. (default: `refseq.file = NULL`).
`refSeqFile`	Deprecated. Use `refseq.file` instead.
`tree.file`	a single `character` value defining the file path of the phylogenetic tree. (default: `tree.file = NULL`).
`phyTreeFile`	Deprecated. Use `tree.file` isntead.
`...`	additional arguments: `temp.dir`: the temporary directory used for decompressing the data. (default: `tempdir()`) `prefix.rm`: `TRUE` or `FALSE`: Should taxonomic prefixes be removed? (default: `prefix.rm = FALSE`)
`file`	character, path of the input qza file. Only files in format of `BIOMV210DirFmt` (feature table), `TSVTaxonomyDirectoryFormat` (taxonomic table), `NewickDirectoryFormat` (phylogenetic tree ) and `DNASequencesDirectoryFormat` (representative sequences) are supported right now.
`temp.dir`	character, a temporary directory in which the qza file will be decompressed to, default `tempdir()`.
`temp`	Deprecated. Use `temp.dir` isntead.

Details

Both arguments as.refseq and refseq.file can be used to define reference sequences of features. as.refseq is only taken into account, if refseq.file is NULL. No reference sequences are tried to be created, if featureNameAsRefSeq is FALSE and refseq.file is NULL.

Value

A TreeSummarizedExperiment object

matrix object for feature table, DataFrame for taxonomic table, ape::phylo object for phylogenetic tree, Biostrings::DNAStringSet for representative sequences of taxa.

Author(s)

Yang Cao

References

Bolyen E et al. 2019: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37: 852–857. https://doi.org/10.1038/s41587-019-0209-9

https://qiime2.org

Examples

assay.file <- system.file("extdata", "table.qza", package = "mia")
row.file <- system.file("extdata", "taxonomy.qza", package = "mia")
col.file <- system.file("extdata", "sample-metadata.tsv", package = "mia")
tree.file <- system.file("extdata", "tree.qza", package = "mia")
refseq.file <- system.file("extdata", "refseq.qza", package = "mia")
tse <- importQIIME2(
  assay.file = assay.file,
  row.file = row.file,
  col.file = col.file,
  refseq.file = refseq.file,
  tree.file = tree.file
)

tse
# Read individual files
assay.file <- system.file("extdata", "table.qza", package = "mia")
row.file <- system.file("extdata", "taxonomy.qza", package = "mia")
col.file <- system.file("extdata", "sample-metadata.tsv", package = "mia")

assay <- importQZA(assay.file)
rowdata <- importQZA(row.file, prefix.rm = TRUE)
coldata <- read.table(col.file, header = TRUE, sep = "\t", comment.char = "")

# Assign rownames 
rownames(coldata) <- coldata[, 1]
coldata[, 1] <- NULL

# Order coldata based on assay
coldata <- coldata[match(colnames(assay), rownames(coldata)), ]

# Create SE from individual files
se <- SummarizedExperiment(assays = list(assay), rowData = rowdata, colData = coldata)
se

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