importQIIME2: Import QIIME2 results to 'TreeSummarizedExperiment'

In microbiome/mia: Microbiome analysis

Import QIIME2 results to TreeSummarizedExperiment

Description

Results exported from QIMME2 can be imported as a TreeSummarizedExperiment using importQIIME2. Except for the featureTableFile, the other data types, taxonomyTableFile, refSeqFile and phyTreeFile, are optional, but are highly encouraged to be provided.

Import the QIIME2 artifacts to R.

Usage

importQIIME2(
  featureTableFile,
  taxonomyTableFile = NULL,
  sampleMetaFile = NULL,
  featureNamesAsRefSeq = TRUE,
  refSeqFile = NULL,
  phyTreeFile = NULL,
  ...
)

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

Arguments

featureTableFile	a single character value defining the file path of the feature table to be imported.
taxonomyTableFile	a single character value defining the file path of the taxonomy table to be imported. (default: taxonomyTableFile = NULL).
sampleMetaFile	a single character value defining the file path of the sample metadata to be imported. The file has to be in tsv format. (default: sampleMetaFile = NULL).
featureNamesAsRefSeq	TRUE or FALSE: Should the feature names of the feature table be regarded as reference sequences? This setting will be disregarded, if refSeqFile is not NULL. If the feature names do not contain valid DNA characters only, the reference sequences will not be set.
refSeqFile	a single character value defining the file path of the reference sequences for each feature. (default: refSeqFile = NULL).
phyTreeFile	a single character value defining the file path of the phylogenetic tree. (default: phyTreeFile = NULL).
...	additional arguments: temp: the temporary directory used for decompressing the data. (default: tempdir()) removeTaxaPrefixes: TRUE or FALSE: Should taxonomic prefixes be removed? (default: removeTaxaPrefixes = 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	character, a temporary directory in which the qza file will be decompressed to, default tempdir().

Details

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

See Also

makeTreeSEFromPhyloseq makeTreeSEFromBiom makeTreeSEFromDADA2 importMothur

Examples

featureTableFile <- system.file("extdata", "table.qza", package = "mia")
taxonomyTableFile <- system.file("extdata", "taxonomy.qza", package = "mia")
sampleMetaFile <- system.file("extdata", "sample-metadata.tsv", package = "mia")
phyTreeFile <- system.file("extdata", "tree.qza", package = "mia")
refSeqFile <- system.file("extdata", "refseq.qza", package = "mia")
tse <- importQIIME2(
  featureTableFile = featureTableFile,
  taxonomyTableFile = taxonomyTableFile,
  sampleMetaFile = sampleMetaFile,
  refSeqFile = refSeqFile,
  phyTreeFile = phyTreeFile
)

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

assay <- importQZA(featureTableFile)
rowdata <- importQZA(taxonomyTableFile, removeTaxaPrefixes = TRUE)
coldata <- read.table(sampleMetaFile, 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

microbiome/mia documentation built on April 27, 2024, 4:04 a.m.