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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
  1. The name and description of function of GenABEL in each group