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

[Package mia version 1.2.7 Index]