GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

[Up] [Top]

Documentation for package ‘GENESIS’ version 2.8.1

Help Pages

GENESIS-package GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
admixMapMM admixMapMM
assocTestMM SNP Genotype Association Testing with Mixed Models
assocTestSeq Aggregate Association Testing with Sequencing Data
assocTestSeqWindow Aggregate Association Testing with Sequencing Data in Sliding Windows
fitNullMM Fit a Mixed Model Under the Null Hypothesis
fitNullReg Fit a Regression Model Under the Null Hypothesis
GENESIS GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
HapMap_ASW_MXL_KINGmat Matrix of Pairwise Kinship Coefficient Estimates for the combined HapMap ASW and MXL Sample found with the KING-robust estimator from the KING software.
king2mat Convert KING text output to an R Matrix
pcair PC-AiR: Principal Components Analysis in Related Samples
pcairPartition Partition a sample into an ancestry representative 'unrelated subset' and a 'related subset'
pcrelate PC-Relate: Model-Free Estimation of Recent Genetic Relatedness
pcrelateMakeGRM Creates a Genetic Relationship Matrix (GRM) of Pairwise Kinship Coefficient Estimates from PC-Relate Output
pcrelateReadInbreed Create a Table of Inbreeding Coefficient Estimates from PC-Relate Output
pcrelateReadKinship Create a Table of Pairwise Kinship Coefficient and IBD Sharing Probability Estimates from PC-Relate Output
plot.pcair PC-AiR: Plotting PCs
print.pcair PC-AiR: Principal Components Analysis in Related Samples
print.summary.pcair PC-AiR: Principal Components Analysis in Related Samples
summary.pcair PC-AiR: Principal Components Analysis in Related Samples
varCompCI Variance Component Confidence Intervals