Package index • ctwas

All functions

add_pos(): Add SNP and gene positions to cTWAS finemapping result.
anno_finemap_res(): Map finemapping result of molecular traits to genes.
anno_susie_alpha_res(): Map molecular traits to genes in susie alpha result.
assemble_region_data(): Assembles data for all the regions
check_n_snps(): Check the numbers of SNPs in snp_map, z_snp and weights
combine_gene_pips(): Combines gene PIPs by context, type or group.
compute_enrichment_test(): Computes enrichment (log-scale), standard error and p-value
compute_gene_z(): Computes z-scores of molecular traits
compute_region_cor(): Computes correlation matrices for a single region
compute_region_nonSNP_PIPs(): Computes non-SNP PIPs for all regions from finemapping result
compute_weight_LD_from_ref(): Computes LD for weight variants using reference LD
convert_fusion_to_predictdb(): Converts fusion weights to predictDB format
convert_geno_to_LD_matrix(): Converts PLINK genotype data to LD matrices and SNP info files, saves LD matrices as .RDS files and SNP info as .Rvar files
convert_predictdb_weights_varIDs(): Convert rsIDs and varIDs in predictDB weights to the reference variant format.
convert_to_ukb_varIDs(): Convert variant IDs from Open GWAS format or PredictDB weight format
create_predictdb_from_QTLs(): Creates weight files in PredictDB format from QTL data
create_snp_LD_map(): Map SNPs to regions using region meta table.
create_snp_map(): Map SNPs to regions using all the variants in the LD reference.
ctwas_sumstats(): cTWAS analysis using summary statistics
ctwas_sumstats_noLD(): cTWAS analysis using summary statistics with "no LD" version
diagnose_LD_mismatch_susie(): Diagnose LD mismatch using SuSiE RSS
est_param(): Estimates cTWAS parameters using EM with cTWAS SER model
estimate_region_L(): Estimate L for all regions by running finemapping with uniform prior
expand_region_data(): Expands region_data with all SNPs
filter_z_gene_by_group_size(): Filter z_gene by group size
finemap_regions(): Runs cTWAS fine-mapping for regions
finemap_regions_noLD(): Runs cTWAS fine-mapping for regions without LD (L = 1)
get_boundary_genes(): Get cross-boundary genes.
get_gene_annot_from_ens_db(): Get gene annotation table from Ensembl database
get_gene_info(): Get gene info from weights.
get_molecular_ids(): Get original molecular IDs
get_predictdb_genome_build(): Get genome build of PredictDB weight
get_problematic_genes(): Gets problematic genes from problematic SNPs
get_region_cor(): Gets correlation matrices for a single region.
load_LD(): Load LD matrix
load_fusion_weights(): Loads weights in FUSION format
load_predictdb_weights(): Loads weights in PredictDB format
load_region_cor(): Loads precomputed correlation matrices for a single region.
load_weights(): Loads weights in PredictDB or FUSION format
make_convergence_plots(): Make convergence plots for the estimated parameters
make_locusplot(): Plots the cTWAS result for a single locus
map_gene_regions(): Map regions for each gene.
merge_region_data(): Merges region data for cross-boundary genes
merge_region_data_noLD(): Merges region data for cross-boundary genes without using LD
postprocess_LD_mismatch(): Runs cTWAS post-processing procedure for merging regions
postprocess_region_merging(): Runs cTWAS post-processing procedure for region merging
postprocess_region_merging_noLD(): Runs cTWAS post-processing procedure for region merging without LD
preprocess_weights(): Preprocess PredictDB/FUSION weights and harmonize with LD reference
preprocess_z_snp(): Preprocess GWAS z-scores, harmonize GWAS z-scores with LD reference
read_gwas(): Read GWAS summary statistics
read_snp_info_file(): Read a single SNP info file as a data frame
read_snp_info_files(): Read multiple single SNP info files as a data frame
screen_regions(): Screens regions with strong signals
select_boundary_genes(): Gets boundary genes and selects high PIP boundary genes
subset_weights(): Get a subset of weights, by group, context or type.
summarize_param(): Summarizes estimated parameters
summarize_region_signals(): Gets a basic summary of region signals
trim_weights(): Trim weights and filter SNPs by LD reference and GWAS SNPs.
update_finemap_res(): Updates cTWAS finemapping result for selected regions
update_merged_region_data(): Updates cTWAS input data with merged region data
update_merged_region_data_noLD(): Updates cTWAS input data without LD with merged region data
update_merged_region_finemap_res(): Updates cTWAS finemapping result for merged regions
update_region_z(): Adds or updates z-scores in region_data based on z_snp and z_gene. this will also update sid and gid based on z_snp and z_gene.
z2p(): convert z-scores to p-values (two-sided test)