importHUMAnN | R Documentation |
TreeSummarizedExperiment
Import HUMAnN results to TreeSummarizedExperiment
file |
|
col.data |
a DataFrame-like object that includes sample names in
rownames, or a single |
colData |
Deprecated. Use |
... |
additional arguments:
|
Import HUMAnN (currently version 3.0 supported) results of functional
predictions based on metagenome composition (e.g. pathways or gene families).
The input must be in merged HUMAnN format. (See
the HUMAnN
documentation and humann_join_tables
method.)
The function parses gene/pathway information along with taxonomy information
from the input file. This information is stored to rowData
. Abundances
are stored to assays
.
Usually the workflow includes also taxonomy data from Metaphlan. See
importMetaPhlAn to load the data to TreeSE
.
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.
importMetaPhlAn
convertFromPhyloseq
convertFromBIOM
convertFromDADA2
importQIIME2
importMothur
# File path
file_path <- system.file("extdata", "humann_output.tsv", package = "mia")
# Import data
tse <- importHUMAnN(file_path)
tse
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