Table 1 GWA analyses grouping
From: ParallABEL: an R library for generalized parallelization of genome-wide association studies
function name of GenABEL | Description | group |
|---|---|---|
summary.snp.data | Provides summary of observed genotypes, allelic frequency, genotypic distribution, P-value of the exact test for HWE and chromosome | 1 |
qtscore | Fast score test for association between a trait and genetic polymorphism | 1 |
mlreg | Linear and logistic regression and Cox models for genome-wide SNP data | 1 |
mmscore | Score test for association between a trait and genetic polymorphism, in samples of related individuals | 1 |
perid.summary | Produces call rate and heterozygosity per person | 2 |
hom | Computes average homozygosity (inbreeding) for a set of people, across multiple markers. Can be used for Quality Control (e.g. contamination checks) | 2 |
ibs | Given a set of SNPs, computes a matrix of average IBS for a group of people | 3 |
dprfast | Given a set of SNPs, computes a matrix of D' | 4 |
rhofast | Given a set of SNPs, computes a matrix of rho | 4 |
r2fast | Given a set of SNPs, computes a matrix of r2 | 4 |