RVPedigree: A package for region-based genetic association tests.

Description

The RVPedigree package contains three methods for doing region-based association tests. It contains methods to perform autosomal rare variant association analyses with a normally-distributed or non normally distributed quantitative phenotype, specifically for the situation when there are related individuals or families in the data. The methods included are:

  • ASKAT (exact test)

  • Normalized ASKAT (exact test)

  • VC-C1 (exact test)

  • VC-C2 (permutation test of VC-C1 statistic)

  • VC-C3 (permutation test of VC-C1 statistic)

RVPedigree functions

The following functions are the user-visible functions of the package:

  • RVPedigree: main function that runs the selected test (ASKAT by default) genome-wide. If you only want to run a given test on a single genomic region, use one of the following functions.

  • ASKAT.region: Runs the ASKAT test on a given genomic region.

  • NormalizedASKAT.region: Runs the Normalized ASKAT test on a given genomic region.

  • VCC1.region: Runs the VC-C1 test on a given genomic region.

  • VCC2.region: Runs the VC-C2 test on a given genomic region.

  • VCC3.region: Runs the VC-C3 test on a given genomic region.

  • Estim.H0.ASKAT: Estimates the null model for the ASKAT test. The result of this function can be passed to the corresponding ASKAT.region function to save computation time in case multiple genomics regions are to be analyzed.

  • Estim.H0.NormalizedASKAT: Estimates the null model for the Normalized ASKAT test. The result of this function can be passed to the corresponding NormalizedASKAT.region function to save computation time in case multiple genomics regions are to be analyzed.

  • Estim.H0.VCC: Estimates the null model for the VC-C1, VC-C2 and VC-C3 tests. The result of this function can be passed to the corresponding VCC?.region function to save computation time in case multiple genomics regions are to be analyzed.

  • GetRelMatrix: calculates the relationship matrix (twice the kinship matrix) based on various types of input data.

  • readMapFile: reads a genetic map file (e.g. from Plink data) and creates the correct data frame to pass on to the various *.region functions.

  • Normality.test: function to test for the normality of the phenotype data.

See Also

GenABEL, snpStats

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