allele.recode

Allele recoding

asplot

Regional association plot

cis.vs.trans.classification

A cis/trans classifier

ReadGRMBin

A function to read GRM binary files

cnvplot

genomewide plot of CNVs

circos.cnvplot

circos plot of CNVs.

circos.cis.vs.trans.plot

circos plot of cis/trans classification

ccsize

Power and sample size for case-cohort design

chow.test

Chow's test for heterogeneity in two regressions

cs

Credible set

comp.score

score statistics for testing genetic linkage of quantitative trait

gcontrol

genomic control

gc.lambda

Estimation of the genomic control inflation statistic (lambda)

gc.em

Gene counting for haplotype analysis

h2.jags

Heritability estimation based on genomic relationship matrix using JAGS

grid2d

Two-dimensional grid

get_b_se

Get b and se from AF, n, and z

get_pve_se

Get pve and its standard error from n, z

gap

Genetic analysis package

circos.mhtplot2

Another circos Manhattan plot

circos.mhtplot

circos Manhattan plot with gene annotation

gcontrol2

genomic control based on p values

snpHWE

Functions for single nucleotide polymorphisms

hap.em

Gene counting for haplotype analysis

genecounting

Gene counting for haplotype analysis

hap.score

Score statistics for association of traits with haplotypes

h2G

Heritability and its variance

ci2ms

Effect size and standard error from confidence interval

chr_pos_a1_a2

SNP id by chr:pos+a1/a2

h2GE

Heritability and its variance when there is an environment component

gcp

Permutation tests using GENECOUNTING

h2l

Heritability under the liability threshold model

h2_mzdz

Heritability estimation according to twin correlations

hg19

Chromosomal lengths for build 37

geno.recode

Genotype recoding

hg18

Chromosomal lengths for build 36

hwe.hardy

Hardy-Weinberg equilibrium test using MCMC

kin.morgan

kinship matrix for simple pedigree

hwe.cc

A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies

invnormal

Inverse normal transformation

ixy

Conversion of chrosome name from strings

makeped

A function to prepare pedigrees in post-MAKEPED format

fbsize

Sample size for family-based linkage and association design

metareg

Fixed and random effects model for meta-analysis

metap

Meta-analysis of p values

klem

Haplotype frequency estimation based on a genotype table of two multiallelic markers

masize

Sample size calculation for mediation analysis

hap

Haplotype reconstruction

hap.control

Control for haplotype reconstruction

mhtplot2

Manhattan plot with annotations

mhtplot.trunc

Truncated Manhattan plot

hwe.jags

Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS

logp

log(p) for a normal deviate z

mia

Multiple imputation analysis for hap

log10pvalue

log10(p) for a P value including its scientific format

mht.control

Controls for mhtplot

inv_chr_pos_a1_a2

Retrieval of chr:pos+a1/a2 according to SNP id

miamiplot

Miami plot

pbsize2

Power for case-control association design

pedtodot_verbatim

Pedigree-drawing with graphviz

pfc.sim

Probability of familial clustering of disease

pedtodot

Converting pedigree(s) to dot file(s)

qtl3dplotly

3D QTL plot

qtl2dplotly

2D QTL plotly

pgc

Preparing weight for GENECOUNTING

g2a

Conversion of a genotype identifier to alleles

miamiplot2

Miami Plot

qtl2dplot

2D QTL plot

mr

Mendelian randomization analysis

pfc

Probability of familial clustering of disease

qqunif

Q-Q plot for uniformly distributed random variable

hg38

Chromosomal lengths for build 38

gif

Kinship coefficient and genetic index of familiality

get_sdy

Get sd(y) from AF, n, b, se

hmht.control

Controls for highlights

log10p

log10(p) for a normal deviate z

mhtplot

Manhattan plot

hwe

Hardy-Weinberg equlibrium test for a multiallelic marker

labelManhattan

Annotate Manhattan or Miami Plot

mtdt2

Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry model

plot.hap.score

Plot haplotype frequencies versus haplotype score statistics

whscore

Whittemore-Halpern scores for allele-sharing

tscc

Power calculation for two-stage case-control design

muvar

Means and variances under 1- and 2- locus (biallelic) QTL model

htr

Haplotype trend regression

mvmeta

Multivariate meta-analysis based on generalized least squares

qtlClassifier

A QTL cis/trans classifier

revStrand

Allele on the reverse strand

read.ms.output

A utility function to read ms output

runshinygap

Start shinygap

pbsize

Power for population-based association design

print.hap.score

Print a hap.score object

snptest_sample

A utility to generate SNPTEST sample file

qtlFinder

Distance-based signal identification

mr_forestplot

Mendelian Randomization forest plot

sentinels

Sentinel identification from GWAS summary statistics

s2k

Statistics for 2 by K table

pvalue

P value for a normal deviate

mtdt

Transmission/disequilibrium test of a multiallelic marker

xy

Conversion of chromosome names to strings

qqfun

Quantile-comparison plots

LDkl

LD statistics for two multiallelic markers

ReadGRM

A function to read GRM file

KCC

Disease prevalences in cases and controls

WriteGRMBin

A function to write GRM binary file

METAL_forestplot

forest plot as R/meta's forest for METAL outputs

WriteGRM

A function to write GRM file

LD22

LD statistics for two diallelic markers

MCMCgrm

Mixed modeling with genetic relationship matrices

b2r

Obtain correlation coefficients and their variance-covariances

ESplot

Effect-size plot

FPRP

False-positive report probability

BFDP

Bayesian false-discovery probability

a2g

Allele-to-genotype conversion

bt

Bradley-Terry model for contingency table

ab

Test/Power calculation for mediating effect

AE3

AE model using nuclear family trios