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QUAIL_pipeline()
Main QUAIL pipeline QUAIL vQTL Analysis Pipeline
QUAIL_rank_score_pipeline()
Main QUAIL Rank Score Pipeline
adjust_susie_weights()
Adjust SuSiE Weights
align_variant_names()
Align Variant Names
allele_qc()
Match alleles between target data and reference variants
auto_decision()
Process Credible Set Information and Determine Updating Strategy
batch_load_twas_weights()
Split loaded twas_weights_results into batches based on maximum memory usage
bayes_a_rss_weights()
Use t-distribution as prior.
bayes_a_weights()
Use t-distribution as prior.
bayes_alphabet_rss_weights()
Extract weights from gbayes_rss function
bayes_alphabet_weights()
Extract Coefficients From Bayesian Linear Regression
bayes_c_rss_weights()
Use a rounded spike prior (low-variance Gaussian).
bayes_c_weights()
Use a rounded spike prior (low-variance Gaussian).
bayes_l_rss_weights()
Use laplace/double exponential distribution as prior. This is equivalent to Bayesian LASSO.
bayes_l_weights()
Use laplace/double exponential distribution as prior. This is equivalent to Bayesian LASSO.
bayes_n_rss_weights()
Use Gaussian distribution as prior. Posterior means will be BLUP, equivalent to Ridge Regression.
bayes_n_weights()
Use Gaussian distribution as prior. Posterior means will be BLUP, equivalent to Ridge Regression.
bayes_r_rss_weights()
Use a hierarchical Bayesian mixture model with four Gaussian components. Variances are scaled by 0, 0.0001 , 0.001 , and 0.01 .
bayes_r_weights()
Use a hierarchical Bayesian mixture model with four Gaussian components. Variances are scaled by 0, 0.0001 , 0.001 , and 0.01 .
calculate_xi_correlation()
Calculate Xi Correlation for QR Coefficients
coloc_post_processor()
coloc_post_processor function
coloc_wrapper()
Colocalization Analysis Wrapper
colocboost_analysis_pipeline()
Multi-trait colocalization analysis pipeline
compute_LD()
Compute LD (Linkage Disequilibrium) Correlation Matrix from Genotypes
compute_LD_gcta_cpp()
Compute LD matrix using GCTA-style formula matching the DENTIST binary.
compute_qtl_enrichment()
Implementation of enrichment analysis described in https://doi.org/10.1371/journal.pgen.1006646
corr_filter()
Filter Highly Correlated SNPs
ctwas_ld_loader()
Utility function to load LD in ctwas analyses, to interface with cTWAS package
dentist()
Detect Outliers Using Dentist Algorithm
dentist_from_files()
Run R DENTIST Implementation on DENTIST-format Input Files
dentist_single_window()
Perform DENTIST on a single window
eqtl_region_example
Example eQTL Region Data (Individual-Level)
extract_LD_for_region()
Extract LD matrix and variants for a specific region
extract_cs_info()
Process Credible Sets (CS) from Finemapping Results
extract_flatten_sumstats_from_nested()
Extract Summary Statistics from Nested Data Structure
extract_top_pip_info()
Extract Information for Top Variant from Finemapping Results
filter_X_with_Y()
This function performing filters on X variants based on Y subjects for TWAS analysis. This function checks whether the absence (NA) of certain subjects would lead to monomorphic in some variants in X after removing of these subjects data from X.
filter_molecular_events()
Filter events based on provided context name pattern
filter_variants_by_ld_reference()
Filter variants by LD Reference
find_data()
Utility function to specify the path to access the target list item in a nested list, especially when some list layers in between are dynamic or uncertain.
find_duplicate_variants()
Filter a vector based on a correlation matrix
find_valid_file_path()
Find Valid File Path
fsusie_get_cs()
@title Create Sets Similar to SuSiE Output from fSuSiE Object
fsusie_wrapper()
Wrapper for fsusie Function with Automatic Post-Processing
gbayes_rss()
Bayesian linear regression using summary statistics
get_cormat()
Compute genotype correlation
get_ctwas_meta_data()
Utility function to format meta data dataframe for cTWAS analyses
get_susie_result()
Extract SuSiE Results from Finemapping Data
gwas_finemapping_example
Example GWAS Fine-Mapping Results (SuSiE)
gwas_sumstats_example
Example GWAS Summary Statistics
harmonize_twas()
Function to perform allele flip QC and harmonization on the weights and GWAS against LD for a region. FIXME: GWAS loading function from Haochen for both tabix & column-mapping yml application
lbf_to_alpha()
Applies the 'lbf_to_alpha_vector' function row-wise to a matrix of log Bayes factors to convert them to Single Effect PIP values.
load_LD_matrix()
Load and Process Linkage Disequilibrium (LD) Matrix
load_genotype_region()
Load genotype data for a specific region using vroom for efficiency
load_multicontext_sumstats()
Load and Align Summary Statistics for a Given Gene and Condition
load_multitask_regional_data()
This function loads a mixture data sets for a specific region, including individual-level data (genotype, phenotype, covariate data) or summary statistics (sumstats, LD). Run load_regional_univariate_data and load_rss_data multiple times for different datasets
load_quantile_twas_weights()
Load Quantile TWAS Weights
load_regional_association_data()
Load regional association data
load_regional_functional_data()
Load Regional Functional Association Data
load_regional_multivariate_data()
Load and Preprocess Regional Multivariate Data
load_regional_regression_data()
Load Regional Data for Regression Modeling
load_regional_univariate_data()
Load Regional Univariate Association Data
load_rss_data()
Load summary statistic data
load_tsv_region()
Load and filter tabular data with optional region subsetting
load_twas_weights()
Load, Validate, and Consolidate TWAS Weights from Multiple RDS Files
manhattan_plot()
Manhattan plot
merge_sumstats_matrices()
Merge a List of Matrices or Data Frames with Optional Allele Flipping
mr_analysis()
Mendelian Randomization (MR)
mr_ash_rss_weights()
Extract weights from mr.ash.rss (susieR)
mr_format()
MR Format Function
mrash_weights()
Compute Weights Using mr.ash Shrinkage
mrmash_wrapper()
Mr.Mash Wrapper
multicontext_ld_clumping()
Perform Clumping and Pruning
multigene_udr()
Perform udr Analysis on Multigene Data
multivariate_analysis_pipeline()
Multivariate Analysis Pipeline
parse_cs_corr()
Parse Credible Set Correlations from extract_cs_info() Output
parse_dentist_output()
Parse DENTIST Binary Output Files
perform_qr_analysis()
Perform Quantile Regression Analysis to get beta
prs_cs()
PRS-CS: a polygenic prediction method that infers posterior SNP effect sizes under continuous shrinkage (CS) priors
prs_cs_weights()
Extract weights from prs_cs function
qr_screen()
Quantile TWAS Weight Calculation and QTL Analysis
qtl_finemapping_example
Example QTL Fine-Mapping Results (SuSiE)
quantile_twas_weight_pipeline()
Quantile TWAS Weight Pipeline
raiss()
Robust and accurate imputation from summary statistics
read_dentist_sumstat()
Read DENTIST-format Summary Statistics
region_to_df()
Utility function to convert LD region_ids to `region of interest` dataframe
rescale_cov_w0()
Re-normalize mrmash weight w0 to have total weight sum to 1
rss_analysis_pipeline()
RSS Analysis Pipeline
rss_basic_qc()
Preprocess input data for RSS analysis
sdpr()
SDPR (Summary-Statistics-Based Dirichelt Process Regression for Polygenic Risk Prediction)
sdpr_weights()
Extract weights from sdpr function
slalom()
Slalom Function for Summary Statistics QC for Fine-Mapping Analysis
summary_stats_qc()
Perform Quality Control on Summary Statistics
susie_post_processor()
Post-process SuSiE Analysis Results
susie_rss_pipeline()
Run the SuSiE RSS pipeline
susie_rss_wrapper()
Wrapper Function for SuSiE RSS with Dynamic L Adjustment
trim_ctwas_variants()
Function to select variants for ctwas weights input
twas_analysis()
TWAS Analysis
twas_joint_z()
Multi-condition TWAS joint test
twas_multivariate_weights_pipeline()
TWAS Multivariate Weights Pipeline
twas_pipeline()
Function to perform TWAS analysis for across multiple contexts. This function peforms TWAS analysis for multiple contexts for imputable genes within an LD region and summarize the twas results.
twas_predict()
Predict outcomes using TWAS weights
twas_weights()
Run multiple TWAS weight methods
twas_weights_cv()
Cross-Validation for weights selection in Transcriptome-Wide Association Studies (TWAS)
twas_weights_pipeline()
TWAS Weights Pipeline
twas_z()
Calculate TWAS z-score and p-value
univariate_analysis_pipeline()
Univariate Analysis Pipeline
venn()
Venn Diagram
xqtl_enrichment_wrapper()
xQTL GWAS Enrichment Analysis
z_to_pvalue()
Convert Z-scores to P-values