Strain Level Microbiome Wide Association Studies

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Documentation for package ‘strainspy’ version 0.99.3

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

Help Pages

abundanceFit	abundanceFit
ani_distance	ani_distance
caseControlFit	caseControlFit
compute_eb_priors	Constructor for strainspy_priors using empirical Bayes estimation
comp_ani_diff_and_posthoc_test	Compute the mean ANI differences for contigs with an identity effect and perform posthoc testing to establish support for each hit.
define_priors	Constructor for strainspy_priors using preset or user defined priors
estimate_beta_diversity	Estimate beta diversity from ANI
estimate_sample_richness	Estimate species richness and coverage of reference strains using ANI
extract_fixef_priors	Access fixef priors needed for ordinal beta regression
extract_fixef_priors-method	Access fixef priors needed for ordinal beta regression
extract_strainspy	Extract data from a StrainSpy 'SummarizedExperiment' object in long format
filter_by_presence	filter_by_presence
getCoefficients	Accessors for strainspy_fit objects
getCoefficients-method	Accessors for strainspy_fit objects
getContigNames	Get Contig names in a fit object
getContigNames-method	Get Contig names in a fit object
getConvergence	Accessors for strainspy_fit objects
getConvergence-method	Accessors for strainspy_fit objects
getDesign	Accessors for strainspy_fit objects
getDesign-method	Accessors for strainspy_fit objects
getFamily	Accessors for strainspy_fit objects
getFamily-method	Accessors for strainspy_fit objects
getFitCall	Accessors for strainspy_fit objects
getFitCall-method	Accessors for strainspy_fit objects
getGenomes	Get Genomes in a fit object
getGenomes-method	Get Genomes in a fit object
getPriorsDf	Access the prior specification table
getPriorsDf-method	Access the prior specification table
getPValues	Accessors for strainspy_fit objects
getPValues-method	Accessors for strainspy_fit objects
getResiduals	Access Residuals
getResiduals-method	Access Residuals
getRowData	Accessors for strainspy_fit objects
getRowData-method	Accessors for strainspy_fit objects
getSamples	Get Sample names in a fit object
getSamples-method	Get Sample names in a fit object
getStdErrors	Accessors for strainspy_fit objects
getStdErrors-method	Accessors for strainspy_fit objects
getVcov	Accessors for strainspy_fit objects
getVcov-method	Accessors for strainspy_fit objects
getZICoefficients	Access Zero-Inflation Coefficients
getZICoefficients-method	Access Zero-Inflation Coefficients
getZIPValues	Accessors for strainspy_fit objects
getZIPValues-method	Accessors for strainspy_fit objects
getZIStdErrors	Accessors for strainspy_fit objects
getZIStdErrors-method	Accessors for strainspy_fit objects
getZIVcov	Accessors for strainspy_fit objects
getZIVcov-method	Accessors for strainspy_fit objects
glmObFit	glmObFit
glmQBFit	glmQBFit
glmZiBFit	glmZiBFit
hadjust	Performs hierarchical taxonomy aware adjustment of p-values.
isScaleContinuous	Accessors for strainspy_fit objects
isScaleContinuous-method	Accessors for strainspy_fit objects
merge_metaphlan_files	merge_metaphlan_files
merge_sourmash_files	merge_sourmash_files
merge_sylph_files	merge_sylph_files
modify_metadata	Add or modify metadata in a 'SummarizedExperiment' object
plot_ani_dist	Generate a violin or box plot for a subset of contigs for a categorical phenotype.
plot_histogram	Generate a histogram for a single contig for a categorical phenotype.
plot_manhattan	Generate a strain Manhattan plot from a strainspy_fit object
plot_mds	Plot MDS of ANI data
plot_pca_biplot	plot_pca_biplot
plot_prior_bootstrap	Plot the bootstrap distributions behind a strainspy_priors object
plot_prior_bootstrap-method	Plot the bootstrap distributions behind a strainspy_priors object
plot_volcano	Generate a Volcano Plot from a strainspy_fit Object
prep_for_prediction	Prepare a caret-compatible prediction data frame from a SummarizedExperiment
read_metaphlan	read_metaphlan
read_sourmash	read_sourmash
read_sylph	Read Sylph query or profile output file and create a SummarizedExperiment object
read_taxonomy	Read and process a taxonomy file
show-method	Show Method for strainspy_fit
show-method	Show method for strainspy_priors objects
strainspy	Strainspy Wrapper
strainspy_fit-accessors	Accessors for strainspy_fit objects
strainspy_fit-class	strainspy_fit: A Class for storing fit data from all strainspy models
strainspy_priors-class	strainspy_priors: A Class for storing model fitting priors
summary-method	Summary Method for strainspy_fit
top_hits	Provides the top results of a strainspy_fit object, sorted by adjusted p-value.