LDtests-package {LDtests} | R Documentation |
Exact tests for Linkage Disequilibrium (LD) and Hardy-Weinberg Equilibrium (HWE). - 2-sided LD tests based on different measures of LD (Kulinskaya and Lewin 2008) - 1-sided Fisher's exact test for LD - 2-sided Haldane test for HWE (Wiggington 2005) - 1-sided test for inbreeding - conditional p-values proposed in Kulinskaya (2008) to overcome the problems of asymetric distributions (for both LD and HWE)
Package: | LDtests |
Type: | Package |
Version: | 1.0 |
Date: | 2008-06-07 |
License: | GPL |
LD2sided.pvals
calculates LD p-values for the input table
Fisher1sided
calculates Fisher's 1-sided p-values for LD for the input table
HWE2sided
calculates HWE p-values for the input table
LD2sided.tables
calculates LD p-values for an entire null distribution
HWE2sided.table
calculates HWE p-values for an entire null distribution
Alex Lewin Maintainer: Alex Lewin <a.m.lewin@imperial.ac.uk>
Kulinskaya and Lewin 2008
ctable <- c(4,5,1,20) LD2sided.tables(ctable) LD2sided.pvals(ctable)$pval.Fish Fisher1sided(ctable)$pval.Fish HWE2sided.table(maf=0.17,n=100) geno <- c(20,73,7) HWE2sided(geno)