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Get or set the info slot from a microEDA object

Source: R/microEDA-class.R
info-accessors.Rd

Accessor methods for either retrieving or setting the info slot in a microEDA object. Additionally, each expected element of the info slot can be retrieved or set individually. Valid keys for the microEDA info slot can be displayed with infoKeys(), while filled info fields of a microEDA object can be displayed with infoFields().

Usage

info(object)

info(object) <- value

infoKeys()

infoFields(object)

taxrank(object)

taxrank(object) <- value

transforms(object)

transforms(object) <- value

# S4 method for class 'microEDA'
mpa_version(object)

# S4 method for class 'microEDA'
mpa_version(object) <- value

filtered_taxa(object)

filtered_taxa(object) <- value

filter_history(object)

filter_history(object) <- value

Arguments

object

A microEDA object.

value

Only used in replacement methods (setters).

For info<-:

A list containing metadata. Valid metadata keys are: 'taxrank', 'transforms', 'filter_history', 'mpa_version'.

For taxrank<-:

A character string specifying the taxonomic rank (e.g., "Species", "Genus").

For transforms<-:

A character vector of applied transformation(s) (e.g., c("TSS", "log2")).

For mpa_version<-:

A character string specifying the MetaPhlAn version (e.g., "#mpa_vJun23_CHOCOPhlAnSGB_202307").

For filtered_taxa<-:

A list with otu_table and tax_table (as matrices) of features that were filtered out.

For filter_history<-:

A named list specifying used filter parameters. Expected elements include:

  • min_abundance: numeric threshold for minimum abundance.

  • min_prevalence: numeric threshold for minimum prevalence.

  • group_var: optional grouping variable for stratified filtering.

  • abundance_criterion: filtering criterion applied to abundance values.

  • group_requirement: filter passing requirement for group-wise filtering.

  • keep_filtered: logical indicating whether filtered-out features were preserved in @info$filtered_taxa.

  • n_removed: integer indicating the number of features removed.

See filter_features for details on filtering arguments.

Value

For info():

A list containing metadata.

For infoKeys():

Lists valid keys for microEDA info slot.

For infoFields():

Lists available field(s) in object info slot.

For taxrank():

A character string with the lowest taxonomic rank.

For transforms():

A character vector of applied transformations.

For mpa_version():

A character string with the used the MetaPhlAn database version.

For filtered_taxa():

A list with otu_table and tax_table of features that were filtered out.

For filter_history():

A list of used filter parameters.

Replacement methods (<-) will return a microEDA object with the updated corresponding slots.

Details

taxrank: represents the lowest available taxonomic rank.

transforms: represents transformation(s) that were applied to the abundance data (otu_table).

mpa_version: represents the MetaPhlAn database version that was used to create the profile.

filtered_taxa: represents the otu_table and tax_table of features that were filtered out.

filter_history: represents filters that were applied to the abundance data (otu_table).

See also

mpa_version,metaphlanProfile-method