loadFromQIIME2 {mia} | R Documentation |
TreeSummarizedExperiment
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.
loadFromQIIME2( featureTableFile, taxonomyTableFile = NULL, sampleMetaFile = NULL, featureNamesAsRefSeq = TRUE, refSeqFile = NULL, phyTreeFile = NULL, ... )
featureTableFile |
a single |
taxonomyTableFile |
a single |
sampleMetaFile |
a single |
featureNamesAsRefSeq |
|
refSeqFile |
a single |
phyTreeFile |
a single |
... |
additional arguments:
|
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
.
A
TreeSummarizedExperiment
object
Yang Cao
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
makeTreeSummarizedExperimentFromPhyloseq
makeSummarizedExperimentFromBiom
makeTreeSummarizedExperimentFromDADA2
loadFromMothur
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