GENetic EStimation and Inference in Structured samples
(GENESIS): Statistical methods for analyzing genetic data from
samples with population structure and/or relatedness
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Documentation for package ‘GENESIS’ version 2.36.0
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| GENESIS-package | GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness |
| admixMap | admixMap |
| admixMapMM | Defunct functions in package 'GENESIS' |
| assocTestAggregate | Aggregate Association Testing |
| assocTestAggregate-method | Aggregate Association Testing |
| assocTestAggregate-methods | Aggregate Association Testing |
| assocTestMM | Defunct functions in package 'GENESIS' |
| assocTestSeq | Defunct functions in package 'GENESIS' |
| assocTestSeqWindow | Defunct functions in package 'GENESIS' |
| assocTestSingle | Genotype Association Testing with Mixed Models |
| assocTestSingle-method | Genotype Association Testing with Mixed Models |
| assocTestSingle-methods | Genotype Association Testing with Mixed Models |
| calcISAFBeta | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness |
| calcScore | Fit a Model Under the Null Hypothesis |
| computeVSIF | Computes variant-specific inflation factors |
| computeVSIFNullModel | Computes variant-specific inflation factors |
| correctK0 | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness |
| correctK2 | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness |
| correctKin | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness |
| effectAllele | Return the effect allele for association testing |
| effectAllele-method | Return the effect allele for association testing |
| effectAllele-methods | Return the effect allele for association testing |
| fitNullMM | Defunct functions in package 'GENESIS' |
| fitNullModel | Fit a Model Under the Null Hypothesis |
| fitNullModel-method | Fit a Model Under the Null Hypothesis |
| fitNullModel-methods | Fit a Model Under the Null Hypothesis |
| fitNullModelFastScore | Fit a Model Under the Null Hypothesis |
| fitNullModelFastScore-method | Fit a Model Under the Null Hypothesis |
| fitNullModelFastScore-methods | Fit a Model Under the Null Hypothesis |
| fitNullReg | Defunct functions in package 'GENESIS' |
| GENESIS | GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness |
| GENESIS-defunct | Defunct functions in package 'GENESIS' |
| 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. |
| isNullModelFastScore | Fit a Model Under the Null Hypothesis |
| isNullModelSmall | Fit a Model Under the Null Hypothesis |
| jointScoreTest | Perform a joint score test |
| kin2gds | Store kinship matrix in GDS |
| king2mat | Defunct functions in package 'GENESIS' |
| kingToMatrix | Convert KING text output to an R Matrix |
| kingToMatrix-method | Convert KING text output to an R Matrix |
| makeSparseMatrix | Make a sparse matrix from a dense matrix or a table of pairwise values |
| makeSparseMatrix-method | Make a sparse matrix from a dense matrix or a table of pairwise values |
| makeSparseMatrix-methods | Make a sparse matrix from a dense matrix or a table of pairwise values |
| mat2gds | Store kinship matrix in GDS |
| nullModelFastScore | Fit a Model Under the Null Hypothesis |
| nullModelInvNorm | Fit a Model Under the Null Hypothesis |
| nullModelSmall | Fit a Model Under the Null Hypothesis |
| pcair | PC-AiR: Principal Components Analysis in Related Samples |
| pcair-method | PC-AiR: Principal Components Analysis in Related Samples |
| pcair-methods | 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 |
| pcrelate-method | Defunct functions in package 'GENESIS' |
| pcrelate-method | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness |
| pcrelateMakeGRM | Defunct functions in package 'GENESIS' |
| pcrelateReadInbreed | Defunct functions in package 'GENESIS' |
| pcrelateReadKinship | Defunct functions in package 'GENESIS' |
| pcrelateSampBlock | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness |
| pcrelateToMatrix | Creates a Genetic Relationship Matrix (GRM) of Pairwise Kinship Coefficient Estimates from PC-Relate Output |
| pcrelateToMatrix-method | Creates a Genetic Relationship Matrix (GRM) of Pairwise Kinship Coefficient 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 |
| samplesGdsOrder | PC-Relate: Model-Free Estimation of Recent Genetic Relatedness |
| sample_annotation_1KG | Annotation for 1000 genomes Phase 3 samples |
| summary.pcair | PC-AiR: Principal Components Analysis in Related Samples |
| varCompCI | Variance Component Confidence Intervals |