Bradley-Terry model for contingency table
Regional association plot
A function to read GRM binary files
circos Manhattan plot with gene annotation
Another circos Manhattan plot
Functions for single nucleotide polymorphisms
Power and sample size for case-cohort design
SNP id by chr:pos+a1/a2
A function to write GRM file
A function to write GRM binary file
Effect size and standard error from confidence interval
genomewide plot of CNVs
Chow's test for heterogeneity in two regressions
cis.vs.trans.classification
A cis/trans classifier
Conversion of a genotype identifier to alleles
Test/Power calculation for mediating effect
circos plot of cis/trans classification
Sample size for family-based linkage and association design
Estimation of the genomic control inflation statistic (lambda)
Genetic analysis package
Two-dimensional grid
score statistics for testing genetic linkage of quantitative trait
Heritability and its variance
Gene counting for haplotype analysis
Heritability and its variance when there is an environment component
Chromosomal lengths for build 38
Heritability estimation according to twin correlations
Credible set
Heritability under the liability threshold model
Controls for highlights
Heritability estimation based on genomic relationship matrix using JAGS
Get b and se from AF, n, and z
Haplotype trend regression
Gene counting for haplotype analysis
genomic control
Get sd(y) from AF, n, b, se
Get pve and its standard error from n, z
Kinship coefficient and genetic index of familiality
Gene counting for haplotype analysis
Hardy-Weinberg equlibrium test for a multiallelic marker
Meta-analysis of p values
Controls for mhtplot
Annotate Manhattan or Miami Plot
Conversion of chrosome name from strings
Inverse normal transformation
circos plot of CNVs.
Truncated Manhattan plot
Mendelian Randomization forest plot
log10(p) for a normal deviate z
Manhattan plot
Transmission/disequilibrium test of a multiallelic marker
Genotype recoding
Fixed and random effects model for meta-analysis
Permutation tests using GENECOUNTING
Retrieval of chr:pos+a1/a2 according to SNP id
Haplotype reconstruction
Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS
genomic control based on p values
log10(p) for a P value including its scientific format
2D QTL plotly
log(p) for a normal deviate z
Score statistics for association of traits with haplotypes
Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry model
Manhattan plot with annotations
Multivariate meta-analysis based on generalized least squares
3D QTL plot
Means and variances under 1- and 2- locus (biallelic) QTL model
Control for haplotype reconstruction
Power for population-based association design
Chromosomal lengths for build 36
A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies
Statistics for 2 by K table
A function to prepare pedigrees in post-MAKEPED format
Hardy-Weinberg equilibrium test using MCMC
Power for case-control association design
Probability of familial clustering of disease
Preparing weight for GENECOUNTING
Sample size calculation for mediation analysis
Converting pedigree(s) to dot file(s)
Q-Q plot for uniformly distributed random variable
Multiple imputation analysis for hap
Miami plot
Sentinel identification from GWAS summary statistics
Chromosomal lengths for build 37
2D QTL plot
Mendelian randomization analysis
Quantile-comparison plots
P value for a normal deviate
Print a hap.score object
Pedigree-drawing with graphviz
Haplotype frequency estimation based on a genotype table of two multiallelic markers
kinship matrix for simple pedigree
Plot haplotype frequencies versus haplotype score statistics
Miami Plot
A QTL cis/trans classifier
Allele on the reverse strand
Start shinygap
Whittemore-Halpern scores for allele-sharing
Probability of familial clustering of disease
A utility to generate SNPTEST sample file
Conversion of chromosome names to strings
A utility function to read ms output
Power calculation for two-stage case-control design
Disease prevalences in cases and controls
AE model using nuclear family trios
A function to read GRM file
Allele recoding
LD statistics for two diallelic markers
Mixed modeling with genetic relationship matrices
LD statistics for two multiallelic markers
False-positive report probability
Bayesian false-discovery probability
Allele-to-genotype conversion
forest plot as R/meta's forest for METAL outputs
Effect-size plot
Obtain correlation coefficients and their variance-covariances