# Differential Abundance Analysis by Consensus

## Documentation for package ‘dar’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

abundance_plt | Abundance boxplot
abundance_plt-method | Abundance boxplot
add_tax | Adds taxonomic level of interest in the Recipe.
add_tax-method | Adds taxonomic level of interest in the Recipe.
add_var | Adds variable of interest to the Recipe
add_var-method | Adds variable of interest to the Recipe
bake | Define consensus strategies from a Recipe
bake-method | Define consensus strategies from a Recipe
contains_rarefaction | Checks if Recipe contains a rarefaction step
cool | Extract results from defined bake
cool-method | Extract results from defined bake
corr_heatmap | Plot otuput of the 'overlap_df' function as a heatmap.
corr_heatmap-method | Plot otuput of the 'overlap_df' function as a heatmap.
exclusion_plt | Plot the number of shared DA OTUs between methods.
exclusion_plt-method | Plot the number of shared DA OTUs between methods.
export_steps | Export step parameters as json.
find_intersections | Finds common OTU between method results
get_phy | Returns phyloseq from Recipe-class object
get_phy-method | Returns phyloseq from Recipe-class object
get_tax | Returns tax_info from Recipe-class object
get_tax-method | Returns tax_info from Recipe-class object
get_var | Returns var_info from Recipe-class object
get_var-method | Returns var_info from Recipe-class object
import_steps | Import steps from json file
intersection_df | Returns data.frame with OTU intersection between methods
intersection_df-method | Returns data.frame with OTU intersection between methods
intersection_plt | Plot results using UpSet plot
intersection_plt-method | Plot results using UpSet plot
metaHIV_phy | Phyloseq object from metaHIV project
mutual_plt | Mutual finding plot
mutual_plt-method | Mutual finding plot
otu_table | Extracts otu_table from phyloseq inside a Recipe
otu_table-method | Extracts otu_table from phyloseq inside a Recipe
overlap_df | Overlap of significant OTUs between tested methods.
overlap_df-method | Overlap of significant OTUs between tested methods.
phyloseq_or_null-class | Recipe-class object
phy_qc | Phyloseq Quality Control Metrics
phy_qc-method | Phyloseq Quality Control Metrics
prep | Performs all the steps defined in a Recipe
prep-method | Performs all the steps defined in a Recipe
PrepRecipe-class | PrepRecipe-class object
rand_id | Make a random identification field for steps
Recipe | Create a Recipe for preprocessing data
recipe | Create a Recipe for preprocessing data
Recipe-class | Recipe-class object
sample_data | Extracts sample_data from phyloseq inside a Recipe
sample_data-method | Extracts sample_data from phyloseq inside a Recipe
show-method | Recipe-class object
steps_ids | Get step_ids from recipe
step_aldex | ALDEx2 analysis
step_aldex-method | ALDEx2 analysis
step_ancom | ANCOM analysis
step_ancom-method | ANCOM analysis
step_corncob | corncob analysis
step_corncob-method | corncob analysis
step_deseq | DESeq2 analysis
step_deseq-method | DESeq2 analysis
step_filter_by_abundance | Filter taxa by abundance
step_filter_by_abundance-method | Filter taxa by abundance
step_filter_by_prevalence | Filter taxa by prevalence
step_filter_by_prevalence-method | Filter taxa by prevalence
step_filter_by_rarity | Filter taxa by rarity
step_filter_by_rarity-method | Filter taxa by rarity
step_filter_by_variance | Filter taxa by variance
step_filter_by_variance-method | Filter taxa by variance
step_filter_taxa | Filter taxa based on across-sample OTU abundance criteria
step_filter_taxa-method | Filter taxa based on across-sample OTU abundance criteria
step_lefse | lefse analysis
step_lefse-method | lefse analysis
step_maaslin | MaAsLin2 analysis
step_maaslin-method | MaAsLin2 analysis
step_metagenomeseq | MetagenomeSeq analysis
step_metagenomeseq-method | MetagenomeSeq analysis
step_rarefaction | Resample an OTU table such that all samples have the same library size.
step_rarefaction-method | Resample an OTU table such that all samples have the same library size.
step_subset_taxa | Subset taxa by taxonomic level
step_subset_taxa-method | Subset taxa by taxonomic level
step_wilcox | Wilcox analysis
step_wilcox-method | Wilcox analysis
tax_table | Extracts tax_table from phyloseq inside a Recipe
tax_table-method | Extracts tax_table from phyloseq inside a Recipe
test_prep_rec | PrepRecipe for metaHIV_phy data
test_rec | Recipe for metaHIV_phy data
tibble_or_NULL-class | Recipe-class object
zero_otu | Extract outs with all 0 values in at least on level of the variable
zero_otu-method | Extract outs with all 0 values in at least on level of the variable