Genetic Analysis Package

[Up] [Top]

Documentation for package ‘gap’ version 1.5-3

Help Pages

A B C E F G H I K L M P Q R S T W X

-- A --

a2g Allele-to-genotype conversion
ab Test/Power calculation for mediating effect
AE3 AE model using nuclear family trios
allele.recode Allele recoding
asplot Regional association plot

-- B --

b2r Obtain correlation coefficients and their variance-covariances
BFDP Bayesian false-discovery probability
bt Bradley-Terry model for contingency table

-- C --

ccsize Power and sample size for case-cohort design
chow.test Chow's test for heterogeneity in two regressions
chr_pos_a1_a2 SNP id by chr:pos+a1/a2
ci2ms Effect size and standard error from confidence interval
circos.cis.vs.trans.plot circos plot of cis/trans classification
circos.cnvplot circos plot of CNVs.
circos.mhtplot circos Manhattan plot with gene annotation
circos.mhtplot2 Another circos Manhattan plot
cis.vs.trans.classification A cis/trans classifier
cnvplot genomewide plot of CNVs
comp.score score statistics for testing genetic linkage of quantitative trait
cs Credible set

-- E --

ESplot Effect-size plot

-- F --

fbsize Sample size for family-based linkage and association design
FPRP False-positive report probability

-- G --

g2a Conversion of a genotype identifier to alleles
gc.em Gene counting for haplotype analysis
gc.lambda Estimation of the genomic control inflation statistic (lambda)
gcontrol genomic control
gcontrol2 genomic control based on p values
gcp Permutation tests using GENECOUNTING
genecounting Gene counting for haplotype analysis
geno.recode Genotype recoding
get_b_se Get b and se from AF, n, and z
get_pve_se Get pve and its standard error from n, z
get_sdy Get sd(y) from AF, n, b, se
gif Kinship coefficient and genetic index of familiality
grid2d Two-dimensional grid

-- H --

h2.jags Heritability estimation based on genomic relationship matrix using JAGS
h2G Heritability and its variance
h2GE Heritability and its variance when there is an environment component
h2l Heritability under the liability threshold model
h2_mzdz Heritability estimation according to twin correlations
hap Haplotype reconstruction
hap.control Control for haplotype reconstruction
hap.em Gene counting for haplotype analysis
hap.score Score statistics for association of traits with haplotypes
hg18 Chromosomal lengths for build 36
hg19 Chromosomal lengths for build 37
hg38 Chromosomal lengths for build 38
hmht.control Controls for highlights
htr Haplotype trend regression
hwe Hardy-Weinberg equlibrium test for a multiallelic marker
hwe.cc A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies
hwe.hardy Hardy-Weinberg equilibrium test using MCMC
hwe.jags Hardy-Weinberg equlibrium test for a multiallelic marker using JAGS

-- I --

invnormal Inverse normal transformation
inv_chr_pos_a1_a2 Retrieval of chr:pos+a1/a2 according to SNP id
ixy Conversion of chrosome name from strings

-- K --

KCC Disease prevalences in cases and controls
kin.morgan kinship matrix for simple pedigree
klem Haplotype frequency estimation based on a genotype table of two multiallelic markers

-- L --

labelManhattan Annotate Manhattan or Miami Plot
LD22 LD statistics for two diallelic markers
LDkl LD statistics for two multiallelic markers
log10p log10(p) for a normal deviate z
log10pvalue log10(p) for a P value including its scientific format
logp log(p) for a normal deviate z

-- M --

makeped A function to prepare pedigrees in post-MAKEPED format
masize Sample size calculation for mediation analysis
MCMCgrm Mixed modeling with genetic relationship matrices
METAL_forestplot forest plot as R/meta's forest for METAL outputs
metap Meta-analysis of p values
metareg Fixed and random effects model for meta-analysis
mht.control Controls for mhtplot
mhtplot Manhattan plot
mhtplot.trunc Truncated Manhattan plot
mhtplot2 Manhattan plot with annotations
mia Multiple imputation analysis for hap
miamiplot Miami plot
miamiplot2 Miami Plot
mr Mendelian randomization analysis
mr_forestplot Mendelian Randomization forest plot
mtdt Transmission/disequilibrium test of a multiallelic marker
mtdt2 Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry model
muvar Means and variances under 1- and 2- locus (biallelic) QTL model
mvmeta Multivariate meta-analysis based on generalized least squares

-- P --

PARn Functions for single nucleotide polymorphisms
pbsize Power for population-based association design
pbsize2 Power for case-control association design
pedtodot Converting pedigree(s) to dot file(s)
pedtodot_verbatim Pedigree-drawing with graphviz
pfc Probability of familial clustering of disease
pfc.sim Probability of familial clustering of disease
pgc Preparing weight for GENECOUNTING
plot.hap.score Plot haplotype frequencies versus haplotype score statistics
print.hap.score Print a hap.score object
pvalue P value for a normal deviate

-- Q --

qqfun Quantile-comparison plots
qqunif Q-Q plot for uniformly distributed random variable
qtl2dplot 2D QTL plot
qtl2dplotly 2D QTL plotly
qtl3dplotly 3D QTL plot
qtlClassifier A QTL cis/trans classifier

-- R --

read.ms.output A utility function to read ms output
ReadGRM A function to read GRM file
ReadGRMBin A function to read GRM binary files
revStrand Allele on the reverse strand
runshinygap Start shinygap

-- S --

s2k Statistics for 2 by K table
sentinels Sentinel identification from GWAS summary statistics
snpHWE Functions for single nucleotide polymorphisms
snpPAR Functions for single nucleotide polymorphisms
snpPVE Functions for single nucleotide polymorphisms
snptest_sample A utility to generate SNPTEST sample file

-- T --

tscc Power calculation for two-stage case-control design

-- W --

whscore Whittemore-Halpern scores for allele-sharing
WriteGRM A function to write GRM file
WriteGRMBin A function to write GRM binary file

-- X --

xy Conversion of chromosome names to strings