loadFromQIIME2 {mia}

R Documentation

Import QIIME2 results to TreeSummarizedExperiment

Description

Results exported from QIMME2 can be imported as a TreeSummarizedExperiment using loadFromQIIME2. Except for the featureTableFile, the other data types, taxonomyTableFile, refSeqFile and phyTreeFile, are optional, but are highly encouraged to be provided.

Usage

loadFromQIIME2(
  featureTableFile,
  taxonomyTableFile = NULL,
  sampleMetaFile = NULL,
  featureNamesAsRefSeq = TRUE,
  refSeqFile = NULL,
  phyTreeFile = NULL,
  ...
)

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)

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

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

makeTreeSummarizedExperimentFromPhyloseq makeSummarizedExperimentFromBiom makeTreeSummarizedExperimentFromDADA2 loadFromMothur

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 <- loadFromQIIME2(
  featureTableFile = featureTableFile,
  taxonomyTableFile = taxonomyTableFile,
  sampleMetaFile = sampleMetaFile,
  refSeqFile = refSeqFile,
  phyTreeFile = phyTreeFile
)

tse

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