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

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_maaslin(): MaAsLin2 analysis

step_metagenomeseq(): MetagenomeSeq analysis

step_wilcox(): Wilcox analysis

Exploration

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 Getters and Adders

add_tax(): Adds taxonomic level of interest in the Recipe.

add_var(): Adds variable of interest to the Recipe

get_phy(): Returns phyloseq from Recipe-class object

get_tax(): Returns tax_info from Recipe-class object

get_var(): Returns var_info from Recipe-class object

otu_table(): Extracts otu_table from phyloseq inside a Recipe

phy_qc(): Phyloseq Quality Control Metrics

sample_data(): Extracts sample_data from phyloseq inside a Recipe

steps_ids(): Get step_ids from recipe

tax_table(): Extracts tax_table from phyloseq inside a Recipe

required_deps(): Returns required pakcages for Recipe object

zero_otu(): Extract outs with all 0 values in at least on level of the variable

Import and Export

export_steps(): Export step parameters as json.

import_steps(): Import steps from json file

read_data() validate_otu() validate_sample_data() validate_tax_table() validate_phyloseq() read_phyloseq() read_file(): Loads Phyloseq data

Other functions

contains_rarefaction(): Checks if Recipe contains a rarefaction step

rand_id(): Make a random identification field for steps

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