Package index • dar

Basic Functions

dar dar-package: dar: Differential Abundance Analysis by Consensus
recipe(): Create a Recipe for preprocessing data
prep(): Performs all the steps defined in a Recipe
bake(): Define consensus strategies from a Recipe
cool(): Extract results from defined bake

Model Configuration

add_model(): Add a centralized statistical model to a recipe
get_model(): Get the centralized statistical model from a recipe

Quality Control

recipe_qc(): Recipe quality-control metrics

Step Functions - Data Preprocessing

step_filter_taxa(): Filter taxa based on across-sample OTU abundance criteria
step_filter_by_prevalence(): Filter taxa by prevalence
step_filter_by_abundance(): Filter taxa by abundance
step_filter_by_rarity(): Filter taxa by rarity
step_filter_by_variance(): Filter taxa by variance
step_subset_taxa(): Subset taxa by taxonomic level
step_rarefaction(): Resample an OTU table such that all samples have the same library size.

Step Functions - Differential Abundance Methods

step_aldex(): ALDEx2 analysis
step_ancom(): ANCOM analysis
step_corncob(): corncob analysis
step_deseq(): DESeq2 analysis
step_lefse(): lefse analysis
step_linda(): LinDA differential-abundance analysis
step_maaslin(): MaAsLin3 analysis
step_wilcox(): Wilcox analysis

Exploration

tidy_results(): Collect differential-abundance results in a tidy contract
abundance_plt(): Abundance boxplot
corr_heatmap(): Plot otuput of the overlap_df function as a heatmap.
exclusion_plt(): Plot the number of shared DA OTUs between methods.
find_intersections(): Finds common OTU between method results
intersection_df(): Returns data.frame with OTU intersection between methods
intersection_plt(): Plot results using UpSet plot
mutual_plt(): Mutual finding plot
overlap_df(): Overlap of significant OTUs between tested methods.

Recipe Data Access

get_phy(): Returns phyloseq from Recipe-class object
otu_table(): Extract a canonical count table from a recipe
sample_data(): Extract complete sample metadata from a recipe
steps_ids(): Get step_ids from recipe
tax_table(): Extract complete taxonomy from a recipe
required_deps(): Returns required pakcages for Recipe object

Lifecycle and Migration

Compatibility interfaces; use the centralized model API in new code.

add_var(): Add legacy variables of interest to a recipe
add_tax(): Add a legacy taxonomic level of interest to a recipe
get_var(): Return legacy target information from a recipe
get_tax(): Return legacy taxonomic information from a recipe
phy_qc(): Defunct functions in dar

Import and Export

export_steps(): Export a recipe analysis configuration as versioned JSON
import_steps(): Import a recipe configuration from versioned JSON

Other functions

contains_rarefaction(): Checks if Recipe contains a rarefaction step
rand_id(): Make a random identification field for steps
rarefaction_help(): Information about the Rarefaction process
PrepRecipe-class: PrepRecipe-class object
show(<PrepRecipe>): Recipe-class object

Data

metaHIV_phy: Phyloseq object from metaHIV project
pastry_df: Pastery data for step id generation
test_rec: Recipe for metaHIV_phy data
test_prep_rec: PrepRecipe for metaHIV_phy data