Estimating Absolute Abundance from Microbial Spike-in Controls

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Documentation for package ‘DspikeIn’ version 1.0.0

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

Help Pages

AcceptableRange	Acceptable Range Data
adjusted_prevalence	Adjust Prevalence in a Microbiome Object
adjust_abundance_by_factor	Adjust Abundance by a Custom Factor
adjust_abundance_one_third	Adjust Abundance by a Custom Factor
alluvial_plot	Generate an Alluvial Plot for Microbiome Data
calculate_list_average_scaling_factors	Calculate Sample-specific Average Scaling Factors for Multiple Spike-in Groups
calculate_spikeIn_factors	Calculate Scaling Factors for Spiked Species in Phyloseq or TSE Object
calculate_spike_percentage	Calculate Spike Percentage for Specified Taxa in a Phyloseq or TSE Object
calculate_spike_percentage_list	Calculate Spike-in Percentage for Specified Taxa
calculate_summary_stats_table	Calculate Summary Statistics Table
color_palette	Original, Extended, and Nature-Inspired Color Palette Sequence
conclusion	Compute Summary Statistics for Spiked Species
convert_categorical_to_factors	Convert Categorical Columns to Factors in Sample Data
convert_phyloseq_to_tse	Convert a 'phyloseq' Object to a 'TreeSummarizedExperiment'
convert_to_absolute_counts	Convert Relative ASV/OTU Counts to Absolute Counts
convert_tse_to_phyloseq	Convert a 'TreeSummarizedExperiment' to a 'phyloseq' Object
create_directory	Create a Directory and Optionally Set as Working Directory
create_list	Create a List from a Phyloseq or TSE Object
degree_network	Analyze and Visualize a Microbial Network
detect_common_asvs_taxa	Detect Common ASVs and Taxa from Multiple Phyloseq or TSE Objects
extract_neighbors	Extract First and Second Neighbors of a Target Node
filter_and_split_abundance	Filter and Split Abundance Data by Threshold
get_long_format_data	Convert a Phyloseq or TSE Object into a Long-Format Data Frame
get_otu_table	Extract OTU Tax Metadata from Object
get_phy_tree	Extract Phylogenetic Tree
get_reference_seq	Extract Reference Sequences
get_sample_data	Extract Sample Data
get_sample_sums	Extract Sample Sums from Object
get_tax_table	Extract Taxonomy Table
gm_mean	Calculate Geometric Mean
imbalance_calculate_list_average_scaling_factors	Calculate Per-Sample Scaling Factors for Multiple Spike-in Groups
label	Label Taxonomic Ranks by Hashcode
load_graphml	Load GraphML Without 'id' Conflicts
metadata_full	Metadata for Microbiome Samples
MG_shapes	Predefined Shape Vector for Plot Styling
my_custom_theme	Custom ggplot2 Theme with Consistent Aesthetics
node_level_metrics	Compute and Visualize Node-Level Network Metrics
norm.clr	CLR Normalization (Centered Log-Ratio Transformation)
norm.css	CSS Normalization (Cumulative Sum Scaling)
norm.DESeq	DESeq Normalization with Pseudocount and Integer Conversion
norm.med	Median Normalization
norm.Poisson	Poisson Normalization and Differential Abundance Function
norm.QN	Quantile Normalization (QN) for phyloseq object
norm.rar	Rarefying
norm.rle	RLE Normalization (Relative Log Expression)
norm.TC	TC Normalization (Total Count Scaling)
norm.TMM	TMM Normalization (Trimmed Mean of M component)
norm.tss	TSS Normalization (Total Sum Scaling)
norm.UQ	UQ Normalization (Upper Quartile)
normalization_set	Apply the Selected Normalization Method to the Phyloseq and TSE Objects
perform_and_visualize_DA	Perform and Visualize Differential Abundance Analysis with edgeR or DESeq2
physeq	Example Phyloseq Object with Tree and Reference Sequences
physeq_16SOTU	Example Phyloseq Object for 16S OTUs
physeq_ITSOTU	Example Phyloseq Object for ITS OTUs
plotbar_abundance	Taxa Bar Plot Without Aggregation (Relative or Absolute Abundance)
plot_core_microbiome_custom	Plot Core Microbiome Prevalence Heatmap (Phyloseq & TSE Compatible)
plot_spikein_tree_diagnostic	Spike-in Tree Diagnostic Plot
Pre_processing_hashcodes	Pre-process phyloseq or TSE object based on hashcodes
Pre_processing_species	Pre-process taxa in a phyloseq or TSE object by merging ASVs/OTUs
Pre_processing_species_list	Preprocess and Merge Spike-in Species in a Phyloseq or TSE Object
proportion_adj	Proportionally Adjust Abundance
quadrant_plot	Generate Custom Quadrant Plots for Node Metrics
RandomForest_selected	Select Important ASVs/OTUs Using Random Forest
randomsubsample_Trimmed_evenDepth	Subsampling to an Equal Sequencing Depth
random_subsample_WithReductionFactor	Random Subsampling with Reduction Factor
regression_plot	Create a Regression Plot with Faceting by Range
relativized_filtered_taxa	Filter Taxa from a Phyloseq or TSE Object Based on Custom Thresholds
remove_zero_negative_count_samples	Remove Samples with Zero, Negative Counts, or NA Values and Add Pseudocount
ridge_plot_it	Generate Ridge Plots for Taxonomic Abundance Distribution
set_nf	Set Normalization Factors in the Sample Data of the Phyloseq Object
simulate_network_robustness	Simulate Network Robustness under Node Removal
summ_ASV_OTUID	Summarize ASV Data Based on ASV_ID
summ_count_phyloseq	Summary Statistics of a Phyloseq or TSE Object
summ_phyloseq_sampleID	Generate Summary Statistics for Each Sample
taxa_barplot	Generate a Taxa Barplot with Relative or Absolute Abundance
tidy_phyloseq_tse	Tidy a Phyloseq or TreeSummarizedExperiment Object
tse	Example TreeSummarizedExperiment (TSE) Object with Tree and Reference Sequences
validate_spikein_clade	Validate Spike-In Clade Consistency with NJ Tree and Bootstrap
weight_Network	Analyze and Visualize a Microbial Network