Man pages for Ravages
Rare Variant Analysis and Genetic Simulations
| adjustedCADD_annotation | SNVs and Indels annotation with adjusted CADD scores |
| adjustedCADD_annotation_indels | Indels annotation with adjusted CADD scores |
| adjustedCADD_annotation_SNVs | SNVs annotation with adjusted CADD scores |
| bed.matrix.split.genomic.region | Bed matrix for variants associated to multiple genomic... |
| burden | Linear, logistic or multinomial regression on a genetic score |
| burden.continuous | Linear regression on a genetic score |
| burden.continuous.subscores | Linear regression on a multiple genetic scores within a... |
| burden.mlogit | Logistic or multinomial regression on a genetic score |
| burden.mlogit.subscores | Logistic or multinomial regression on a multiple genetic... |
| burden.subscores | Linear, logistic or multinomial regression on a multiple... |
| burden.weighted.matrix | Score matrix for burden tests |
| CAST | Cohort Allelic Sum Test |
| filter_adjustedCADD | Variant filtering based on frequency and median adjusted CADD... |
| filter.rare.variants | Rare variants filtering |
| genes.positions | Genes positions |
| genotypic.freq | Genotypic frequencies calculation for data simulations |
| GnomADgenes | GnomADgenes dataset |
| GRR.matrix | GRR matrix for genetic data simulation |
| Jaccard | Jaccard index |
| Kryukov | Kryukov data set |
| LCT.haplotypes | LCT haplotypes data set |
| LCT.matrix | LCT genotypes matrix |
| multinomial.asso.freq | Single variant association test with categorical phenotype |
| NullObject.parameters | Null Model for SKAT and burden tests |
| RAVA_FIRST | RAVA-FIRST: RAre Variant Association using... |
| rbm.GRR | Simulation of genetic data using GRR values |
| rbm.GRR.power | Power of RVAT based on simulations and theoretical... |
| rbm.haplos.freqs | Simulation of genetic data based on haplotypic frequencies |
| rbm.haplos.power | Power of RVAT based on simulations with haplotypes |
| rbm.haplos.thresholds | Simulation of genetic data based on haplotypes and a... |
| set.CADDregions | Variants annotation based on 'CADD regions' and genomic... |
| set.genomic.region | Variants annotation based on gene positions |
| set.genomic.region.subregion | Variants annotation based on regions and subregions positions |
| SKAT | SKAT test |
| SKAT.bootstrap | Multi group SKAT test using bootstrap sampling |
| SKAT.continuous | Multi group SKAT test using Liu et al. approximation |
| SKAT.permutations | Multi group SKAT test using bootstrap sampling |
| SKAT.theoretical | Multi group SKAT test using Liu et al. approximation |
| subregions.LCT | Exemple of functional categories |
| WSS | WSS genetic score |
