Function reference
-
annotateGeneName() - annotate the reName4formatDat with gene info
-
area() - Calculate the area under a time-series curve
-
dat4GRAPPLE() - prepare data for implementing MR-GRAPPLE
-
dat4UKBNealeLab() - data processing for UKB-Neale Labs GWAS summary statistics
-
datMerge() - merge the data set based on SNP
-
getAnnotatedSNPs() - Get annotated SNPs info
-
getLDmatrix() - Get LDmatrix for given SNPs concerning 1KG reference
-
getPaths() - get system-specific paths
-
hello() - Hello, World!
-
loadSPSS() - Import data files with SPSS format
-
plt.region() - plot the regional association plot for exp- and out-GWAS
-
plt.stack.region() - plot the regional association plot for exp-, eQTL- and out-GWAS
-
readdeCODEProteomicsGRCh38() - read summary statistics from deCODE using Olink Explore 1536 Panel
-
readHarmonizedGWASCatalogGRCh37() - read harmonized summary statistics from GWAS Catalog
-
readHarmonizedGWASCatalogGRCh37Txt() - read harmonized summary statistics in .txt format from GWAS Catalog
-
rmName4formatDat() - rename TwoSampleMR::format_data() with snps selection at
pval
-
runCisMR() - run drug target (cis-) MR analyses with annotated data
-
runDebiasedMR() - run de-biased MR using TwoSampleMR pkg
-
runGeneMendelianRandomization() - run Gene-based MR analyses with correlated IVs
-
runGRAPPLE() - run three-sample MR using MR-GRAPPLE
-
runMendelianRandomization() - run MR using MendelianRandomization
-
runMRClust() - run MR-Clust analysis
-
runMRClustBest() - run MR analyses based on MR-Clust
-
runMRIVW() - run MR-IVW using TwoSampleMR pkg
-
runMRRAPS() - run MR-RAPS using TwoSampleMR pkg
-
runSuSiERMR() - run MR analysis based on SuSiER
-
run_clump() - run ld clump locally
-
run_SuSiE() - Implement the fine-mapping analysis using SuSiE method