Differential Abundance Analysis by Consensus

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Documentation for package ‘dar’ version 1.3.0

• 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