Import taxpasta-specific BIOM results to TreeSummarizedExperiment

Source: R/importTaxpasta.R

Import taxpasta-specific BIOM results to TreeSummarizedExperiment

importTaxpasta(file, add.tree = TRUE, ...)

Arguments

file

Character scalar. Defines the file path to a BIOM file.

add.tree

Logical scalar. Specifies whether to calculate and add hierarchy tree using addHierarchyTree. (Default: TRUE)

...

additional arguments

  • set.ranks: Logical scalar. Should column names of taxonomy table be treated as taxonomy ranks? (Default: FALSE)

Value

A TreeSummarizedExperiment object.

Details

importTaxpasta imports data that is returned from Taxonomic Profile Aggregation and Standardization (taxpasta) pipeline. See more information on taxpasta from taxpasta documentation.

Examples


if (FALSE) { # \dontrun{
# File path to BIOM file
file_path <- system.file("extdata", "complete.biom", package = "mia")
# Import BIOM as TreeSE, and set ranks.
tse <- importTaxpasta(file_path, set.ranks = TRUE)
# Import BIOM as TreeSE without adding hierarchy tree
tse <- importTaxpasta(file_path, add.tree = FALSE)
} # }