View source: R/importMetaphlan.R
importMetaPhlAn | R Documentation |
TreeSummarizedExperiment
Import Metaphlan results to TreeSummarizedExperiment
file |
|
col.data |
a DataFrame-like object that includes sample names in
rownames, or a single |
colData |
Deprecated. use |
sample_meta |
Deprecated. Use |
tree.file |
|
phy_tree |
Deprecated. Use |
... |
additional arguments:
|
Import Metaphlan (versions 2, 3 and 4 supported) results.
Input must be in merged Metaphlan format.
(See
the Metaphlan documentation and merge_metaphlan_tables
method.)
Data is imported so that data at the lowest rank is imported as a
TreeSummarizedExperiment
object. Data at higher rank is imported as a
SummarizedExperiment
objects which are stored to altExp
of
TreeSummarizedExperiment
object.
Currently Metaphlan versions 2, 3, and 4 are supported.
A
TreeSummarizedExperiment
object
Leo Lahti and Tuomas Borman. Contact: microbiome.github.io
Beghini F, McIver LJ, Blanco-MÃguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, & Segata N (2021) Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife. 10:e65088. doi: 10.7554/eLife.65088
convertFromPhyloseq
convertFromBIOM
convertFromDADA2
importQIIME2
importMothur
# (Data is from tutorial
# https://github.com/biobakery/biobakery/wiki/metaphlan3#merge-outputs)
# File path
file_path <- system.file(
"extdata", "merged_abundance_table.txt", package = "mia")
# Import data
tse <- importMetaPhlAn(file_path)
# Data at the lowest rank
tse
# Data at higher rank is stored in altExp
altExps(tse)
# Higher rank data is in SE format, for example, Phylum rank
altExp(tse, "phylum")
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