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 regions |
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 genomic region |
burden.mlogit |
Logistic or multinomial regression on a genetic score |
burden.mlogit.subscores |
Logistic or multinomial regression on a multiple genetic scores within a genomic region |
burden.subscores |
Linear, logistic or multinomial regression on a multiple genetic scores within a genomic region |
burden.weighted.matrix |
Score matrix for burden tests |
CAST |
Cohort Allelic Sum Test |
filter.adjustedCADD |
Variant filtering based on frequency and median adjusted CADD by CADD regions |
filter.rare.variants |
Rare variants filtering |
genes.b37 |
Genes positions |
genes.b38 |
Genes positions |
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.hap |
LCT haplotypes data set |
LCT.haplotypes |
LCT haplotypes data set |
LCT.matrix |
LCT genotypes matrix |
LCT.matrix.bed |
LCT genotypes matrix |
LCT.matrix.fam |
LCT genotypes matrix |
LCT.matrix.pop1000G |
LCT genotypes matrix |
LCT.sample |
LCT haplotypes data set |
LCT.snps |
LCT haplotypes data set |
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 Functionally-InfoRmed STeps |
rbm.GRR |
Simulation of genetic data using GRR values |
rbm.GRR.power |
Power of RVAT based on simulations and theoretical calculations (CAST) with GRR |
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 libaility model |
set.CADDregions |
Variants annotation based on 'CADD regions' and genomic categories |
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 |