TWAS pipeline refactor and full S4 refactor

DESCRIPTION

@@ -118,7 +118,6 @@ Collate:
     'mrmash_wrapper.R'
     'multitrait_data.R'
     'multivariate_pipeline.R'
-    'otters.R'
     'pval_combine.R'
     'raiss.R'
     'regularized_regression.R'

NAMESPACE

@@ -6,10 +6,13 @@ S3method(postprocess_finemapping_fit,susiF)
 S3method(postprocess_finemapping_fit,susie)
 S3method(postprocess_finemapping_fit,susie_inf)
 S3method(postprocess_finemapping_fit,susie_rss)
+export(AlleleQCResult)
 export(AnnotationMatrix)
 export(FineMappingResult)
 export(GWASSumStats)
 export(LDData)
+export(MultivariateRegionalData)
+export(QCResult)
 export(RegionalData)
 export(TWASWeights)
 export(adjust_susie_weights)
@@ -27,6 +30,7 @@ export(bayes_n_weights)
 export(bayes_r_weights)
 export(build_top_loci)
 export(check_ld)
+export(classify_variant_type)
 export(clean_context_names)
 export(coloc_post_processor)
 export(coloc_wrapper)
@@ -63,33 +67,60 @@ export(filter_relatedness)
 export(filter_variants_by_ld_reference)
 export(find_data)
 export(find_duplicate_variants)
+export(find_overlapping_regions)
 export(fine_mr)
 export(fit_mash_contrast)
+export(fit_susie_inf_then_susie_rss)
 export(format_finemapping_output)
 export(fsusie_get_cs)
 export(fsusie_wrapper)
 export(getBaseline)
 export(getBlockMetadata)
 export(getCS)
+export(getCVPerformance)
 export(getCandidates)
+export(getChrom)
 export(getCorrelation)
+export(getCovariates)
+export(getDataType)
 export(getEffects)
 export(getEnrichment)
+export(getFits)
+export(getGenotypeMatrix)
 export(getGenotypes)
+export(getGrange)
+export(getHarmonizedData)
 export(getLBF)
+export(getLDData)
 export(getLocal)
 export(getMaf)
+export(getMethodNames)
+export(getMolecularId)
 export(getN)
+export(getOutlierNumber)
 export(getPIP)
+export(getPhenotypes)
+export(getPreprocess)
+export(getQCSummary)
+export(getRSSInput)
+export(getRefPanel)
 export(getResidualX)
 export(getResidualXScalar)
 export(getResidualY)
 export(getResidualYScalar)
 export(getScoreStats)
+export(getSkipReason)
+export(getStandardized)
+export(getTopLoci)
+export(getTrimmedFit)
 export(getVarY)
 export(getVariantIds)
 export(getVariantInfo)
+export(getVariantNames)
 export(getWeights)
+export(getXVariance)
+export(getYMatrix)
+export(getYScalar)
 export(getZ)
 export(get_ctwas_meta_data)
 export(get_filter_lbf_index)
@@ -102,6 +133,7 @@ export(harmonize_gwas)
 export(harmonize_twas)
 export(hasGenotypes)
 export(invert_minmax_scaling)
+export(isSkipped)
 export(is_binary_sldsc_annot)
 export(l0learn_rss_weights)
 export(l0learn_weights)
@@ -115,6 +147,7 @@ export(ld_mismatch_qc)
 export(ld_prune_by_correlation)
 export(load_LD_matrix)
 export(load_genotype_region)
+export(load_ld_sketch)
 export(load_multicontext_sumstats)
 export(load_multitask_regional_data)
 export(load_multitrait_R_sumstat)
@@ -149,8 +182,6 @@ export(multivariate_analysis_pipeline)
 export(mvsusie_weights)
 export(nSnps)
 export(normalize_variant_id)
-export(otters_association)
-export(otters_weights)
 export(parse_cs_corr)
 export(parse_region)
 export(parse_variant_id)
@@ -169,6 +200,7 @@ export(region_data_to_colocboost_input)
 export(region_data_to_ind_input)
 export(region_data_to_rss_input)
 export(region_to_df)
+export(regions_overlap)
 export(robust_mahalanobis)
 export(rss_analysis_pipeline)
 export(rss_basic_qc)
@@ -185,9 +217,12 @@ export(standardise_sumstats_columns)
 export(standardize_sldsc_trait)
 export(subsetChr)
 export(summary_stats_qc)
+export(susie_ash_rss_weights)
 export(susie_ash_weights)
+export(susie_inf_rss_weights)
 export(susie_inf_weights)
 export(susie_rss_pipeline)
+export(susie_rss_weights)
 export(susie_weights)
 export(top_loci_to_granges)
 export(trim_ctwas_variants)
@@ -199,6 +234,7 @@ export(twas_predict)
 export(twas_weights)
 export(twas_weights_cv)
 export(twas_weights_pipeline)
+export(twas_weights_sumstat_pipeline)
 export(twas_z)
 export(univariate_analysis_pipeline)
 export(update_mash_model_cov)
@@ -207,6 +243,7 @@ export(writeSumstatsVcf)
 export(xgboost_imputation)
 export(xqtl_enrichment_wrapper)
 export(z_to_pvalue)
+exportClasses(AlleleQCResult)
 exportClasses(AnnotationMatrix)
 exportClasses(FineMappingResult)
 exportClasses(GWASSumStats)
@@ -217,32 +254,61 @@ exportClasses(LDData)
 exportClasses(LDEigen)
 exportClasses(LDScore)
 exportClasses(LDStatistic)
+exportClasses(MultivariateRegionalData)
+exportClasses(QCResult)
 exportClasses(RegionalData)
 exportClasses(TWASWeights)
+exportMethods(c)
 exportMethods(computeLdScores)
 exportMethods(estimateH2)
 exportMethods(getBlockMetadata)
 exportMethods(getCS)
+exportMethods(getCVPerformance)
+exportMethods(getChrom)
 exportMethods(getCorrelation)
+exportMethods(getCovariates)
+exportMethods(getDataType)
 exportMethods(getEffects)
 exportMethods(getEnrichment)
+exportMethods(getFits)
+exportMethods(getGenotypeMatrix)
 exportMethods(getGenotypes)
+exportMethods(getGrange)
+exportMethods(getHarmonizedData)
 exportMethods(getLBF)
+exportMethods(getLDData)
 exportMethods(getLocal)
 exportMethods(getMaf)
+exportMethods(getMethodNames)
+exportMethods(getMolecularId)
 exportMethods(getN)
+exportMethods(getOutlierNumber)
 exportMethods(getPIP)
+exportMethods(getPhenotypes)
+exportMethods(getPreprocess)
+exportMethods(getQCSummary)
+exportMethods(getRSSInput)
+exportMethods(getRefPanel)
 exportMethods(getResidualX)
 exportMethods(getResidualXScalar)
 exportMethods(getResidualY)
 exportMethods(getResidualYScalar)
 exportMethods(getScoreStats)
+exportMethods(getSkipReason)
+exportMethods(getStandardized)
+exportMethods(getTopLoci)
+exportMethods(getTrimmedFit)
 exportMethods(getVarY)
 exportMethods(getVariantIds)
 exportMethods(getVariantInfo)
+exportMethods(getVariantNames)
 exportMethods(getWeights)
+exportMethods(getXVariance)
+exportMethods(getYMatrix)
+exportMethods(getYScalar)
 exportMethods(getZ)
 exportMethods(hasGenotypes)
+exportMethods(isSkipped)
 exportMethods(nSnps)
 exportMethods(readAnnotations)
 exportMethods(readGenotypes)