Man pages for dajiangliu/rareGWAMA
Meta-Analysis of Gene-level Rare Variant Association Test in Whole Genome Datasets
| binary.rareMETALS.single.group | Single variant meta-analysis |
| binom.conf | get binomial confidence intervals via normal approx |
| calcGeneLevelTest | rvmeta.CMH.new which takes ustat, V stat as input; |
| calc.r2 | calculate R2 from a list of variants; |
| colCenter | This function implements function to colCenter a matrix so... |
| ColSums | Safe colSums |
| conditional.rareMETALS.range | Perform conditional analysis for gene-level tests |
| conditional.rareMETALS.range.group | Perform conditional analysis for gene-level tests and... |
| conditional.rareMETALS.single | Perform conditional analysis for single variant tests |
| conditional.rareMETALS.single.group | Perform conditional analysis for single variant tests |
| conditional.rareMETALS.single.group.core | Perform conditional analysis for single variant tests |
| convertChisq2Beta | convert chisq statistic to beta for binary trait assuming the... |
| estimateH2 | Estimate the variance explained by the variants in a locus; |
| find.gene.chrpos | Find the chromosomal position for genes; |
| find.top.variant | Find top variants in a gene region that satisfy a MAF cutoff; |
| flipAllele | This is the function for flipping alleles |
| genomic.dist | Get genomic distance between two variant positions; |
| get.conditional.score.stat | This is the function to obtain conditional score statistics; |
| get.conditional.score.stat.RE | This is the function to obtain conditional score statistics... |
| get.gene.inWindow | Find nearby genes for a sigificant SNP |
| getImpQual | get imputation quality from tables based upon imputation... |
| get.tabix.range | change position to tabix range; |
| GWAMA.formatData | format data into matrices; |
| GWAMA.rmMulti | remove multi-allelic sites; |
| GWAMA.single | Single variant meta-analysis |
| imputeConditional | Impute missing summary association statistics assuming |
| imputeMeta | Impute missing summary association statistics assuming |
| Mean | Safe mean |
| multiAlleleAssoc | Perform multi-allelic association tests; |
| myFormat | format according to publication standard; |
| paste.pos | This function quickly paste chrom and pos; |
| pwrCalc | power calculation |
| rareGWAMA.burden | gene-level test |
| rareGWAMA.cond.gene | conditional analysis for single variant association test; |
| rareGWAMA.cond.single | conditional analysis for single variant association test; |
| rareGWAMA.cond.single.msso | conditional analysis for single variant association test; |
| rareGWAMA.estH2 | Estimate the variance explained; |
| rareGWAMA.formatGene | organize the formatted stat into analyzable format; |
| rareGWAMA.gene | Conduct approximate gene-level tests and estimate variance... |
| rareGWAMA.single | single variant meta-analysis integrating imputation quality; |
| rareGWAMA.single.multiAllele | gateway function for multi-allelic analysis in rareGWAMA |
| rareGWAMA.skat | SKAT test |
| rareGWAMA.t | t test; |
| rareGWAMA.TWAS | perform single tissue twas and multiple tissue twas; |
| rareGWAMA.vt | vt test; |
| rareMETALS.calcGC | calculate GC by frequency bins; |
| rareMETALS.cleanScore | Single variant meta-analysis |
| rareMETALS.estimatePVE | Estimate the variance explained for a list of variants... |
| rareMETALS.gene | Meta-analysis of gene-level tests; |
| rareMETALS.gene.group | Meta-analysis of gene-level tests by range; |
| rareMETALS.parseAnno | A function to pass ANNOFULL from SEQMINER; |
| rareMETALS.range | Meta-analysis of gene-level tests by range; |
| rareMETALS.range.core | #' Meta-analysis of gene-level tests by range; |
| rareMETALS.range.group | Meta-analysis of gene-level tests by range; |
| rareMETALS.range.group.core | Meta-analysis of gene-level tests by range; |
| rareMETALS.single | Single variant meta-analysis |
| rareMETALS.single.correctRefAlt | Single variant meta-analysis |
| rareMETALS.single.group | Single variant meta-analysis |
| regMat | regularize matrix; |
| rm.na | Remove nas |
| RowSums | Safe rowSums |
| rvmeta.CMH | Function that implement gene-level tests |
| set.intersect | Intersection of two sets; |
| sortPos | Sort genomic positions; |
| splitVecByChunkSize | This function implement how to split a vector into chunks of... |
| Sum | Safe sum |
| toMinor | To minor: change number >.5 to 1-# |
| uniq.allele | unique alternative alleles; |
