Package: gap 1.6

gap: Genetic Analysis Package

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

Authors:Jing Hua Zhao [aut, cre], Kurt Hornik [ctb], Brian Ripley [ctb], Uwe Ligges [ctb], Achim Zeileis [ctb]

gap_1.6.tar.gz
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gap.pdf |gap.html✨
gap/json (API)

# Install 'gap' in R:
install.packages('gap', repos = c('https://jinghuazhao.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jinghuazhao/r/issues

Datasets:
  • hg18 - Chromosomal lengths for build 36
  • hg19 - Chromosomal lengths for build 37
  • hg38 - Chromosomal lengths for build 38

On CRAN:

geneticsimputationlmm

109 exports 12 stars 5.05 score 73 dependencies 14 dependents 29 mentions 438 scripts 12.4k downloads

Last updated 6 days agofrom:810f4da678. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-win-x86_64NOTESep 12 2024
R-4.5-linux-x86_64NOTESep 12 2024
R-4.4-win-x86_64NOTESep 12 2024
R-4.4-mac-x86_64NOTESep 12 2024
R-4.4-mac-aarch64NOTESep 12 2024
R-4.3-win-x86_64NOTESep 12 2024
R-4.3-mac-x86_64NOTESep 12 2024
R-4.3-mac-aarch64NOTESep 12 2024

Exports:a2gabAE3allele.recodeasplotb2rBFDPbtccsizechow.testchr_pos_a1_a2ci2mscircos.cis.vs.trans.plotcircos.cnvplotcircos.mhtplotcircos.mhtplot2cis.vs.trans.classificationcnvplotcomp.scorecsESplotfbsizeFPRPg2agc.emgc.lambdagcontrolgcontrol2gcpgenecountinggeno.recodeget_b_seget_pve_seget_sdygifgrid2dh2_mzdzh2.jagsh2Gh2GEh2lhaphap.controlhap.emhap.scorehmht.controlhwehwe.cchwe.hardyhwe.jagsinv_chr_pos_a1_a2invnormalixyKCCkin.morganklemlabelManhattanLD22LDkllog10plog10pvaluelogpmakepedmasizeMCMCgrmMETAL_forestplotmetapmetaregmht.controlmhtplotmhtplot.truncmhtplot2miamiamiplotmiamiplot2mrmr_forestplotmtdtmtdt2muvarmvmetapbsizepbsize2pedtodotpedtodot_verbatimpfcpfc.simpgcpvalueqqfunqqunifqtl2dplotqtl2dplotlyqtl3dplotlyqtlClassifierqtlFinderread.ms.outputReadGRMReadGRMBinrevStrandrunshinygaps2ksentinelssnptest_sampletsccwhscoreWriteGRMWriteGRMBinxy

Dependencies:askpassbase64encbslibcachemclicolorspacecpp11crosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgap.datasetsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlypromisespurrrR6rappdirsrbibutilsRColorBrewerRcppRdpackrlangrmarkdownsassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Genetic Analysis Package

Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, https://jinghuazhao.github.io/

Rendered fromgap.Rmdusingknitr::rmarkdownon Sep 12 2024.

Last update: 2024-04-05
Started: 2021-05-28

gap: genetic analysis package

Rendered fromjss.Rnwusingutils::Sweaveon Sep 12 2024.

Last update: 2021-05-29
Started: 2018-01-23

Shiny for Genetic Analysis Package (gap) Designs

Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK, https://jinghuazhao.github.io/

Rendered fromshinygap.Rmdusingknitr::rmarkdownon Sep 12 2024.

Last update: 2023-08-21
Started: 2021-06-07

Readme and manuals

Help Manual

Help pageTopics
Allele-to-genotype conversiona2g
Test/Power calculation for mediating effectab
AE model using nuclear family triosAE3
Allele recodingallele.recode
Regional association plotasplot
Obtain correlation coefficients and their variance-covariancesb2r
Bayesian false-discovery probabilityBFDP
Bradley-Terry model for contingency tablebt
Power and sample size for case-cohort designccsize
Chow's test for heterogeneity in two regressionschow.test
SNP id by chr:pos+a1/a2chr_pos_a1_a2
Effect size and standard error from confidence intervalci2ms
circos plot of cis/trans classificationcircos.cis.vs.trans.plot
circos plot of CNVs.circos.cnvplot
circos Manhattan plot with gene annotationcircos.mhtplot
Another circos Manhattan plotcircos.mhtplot2
A cis/trans classifiercis.vs.trans.classification
genomewide plot of CNVscnvplot
score statistics for testing genetic linkage of quantitative traitcomp.score
Credible setcs
Effect-size plotESplot
Sample size for family-based linkage and association designfbsize
False-positive report probabilityFPRP
Conversion of a genotype identifier to allelesg2a
Gene counting for haplotype analysisgc.em
Estimation of the genomic control inflation statistic (lambda)gc.lambda
genomic controlgcontrol
genomic control based on p valuesgcontrol2
Permutation tests using GENECOUNTINGgcp
Gene counting for haplotype analysisgenecounting
Genotype recodinggeno.recode
Get b and se from AF, n, and zget_b_se
Get pve and its standard error from n, zget_pve_se
Get sd(y) from AF, n, b, seget_sdy
Kinship coefficient and genetic index of familialitygif
Two-dimensional gridgrid2d
Heritability estimation according to twin correlationsh2_mzdz
Heritability estimation based on genomic relationship matrix using JAGSh2.jags
Heritability and its varianceh2G
Heritability and its variance when there is an environment componenth2GE
Heritability under the liability threshold modelh2l
Haplotype reconstructionhap
Control for haplotype reconstructionhap.control
Gene counting for haplotype analysishap.em
Score statistics for association of traits with haplotypeshap.score
Chromosomal lengths for build 36hg18
Chromosomal lengths for build 37hg19
Chromosomal lengths for build 38hg38
Controls for highlightshmht.control
Haplotype trend regressionhtr
Hardy-Weinberg equlibrium test for a multiallelic markerhwe
A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studieshwe.cc
Hardy-Weinberg equilibrium test using MCMChwe.hardy
Hardy-Weinberg equlibrium test for a multiallelic marker using JAGShwe.jags
Retrieval of chr:pos+a1/a2 according to SNP idinv_chr_pos_a1_a2
Inverse normal transformationinvnormal
Conversion of chrosome name from stringsixy
Disease prevalences in cases and controlsKCC
kinship matrix for simple pedigreekin.morgan
Haplotype frequency estimation based on a genotype table of two multiallelic markersklem
Annotate Manhattan or Miami PlotlabelManhattan
LD statistics for two diallelic markersLD22
LD statistics for two multiallelic markersLDkl
log10(p) for a normal deviate zlog10p
log10(p) for a P value including its scientific formatlog10pvalue
log(p) for a normal deviate zlogp
A function to prepare pedigrees in post-MAKEPED formatmakeped
Sample size calculation for mediation analysismasize
Mixed modeling with genetic relationship matricesMCMCgrm
forest plot as R/meta's forest for METAL outputsMETAL_forestplot
Meta-analysis of p valuesmetap
Fixed and random effects model for meta-analysismetareg
Controls for mhtplotmht.control
Manhattan plotmhtplot
Truncated Manhattan plotmhtplot.trunc
Manhattan plot with annotationsmhtplot2
Multiple imputation analysis for hapmia
Miami plotmiamiplot
Miami Plotmiamiplot2
Mendelian randomization analysismr
Mendelian Randomization forest plotmr_forestplot
Transmission/disequilibrium test of a multiallelic markermtdt
Transmission/disequilibrium test of a multiallelic marker by Bradley-Terry modelmtdt2
Means and variances under 1- and 2- locus (biallelic) QTL modelmuvar
Multivariate meta-analysis based on generalized least squaresmvmeta
Power for population-based association designpbsize
Power for case-control association designpbsize2
Converting pedigree(s) to dot file(s)pedtodot
Pedigree-drawing with graphvizpedtodot_verbatim
Probability of familial clustering of diseasepfc
Probability of familial clustering of diseasepfc.sim
Preparing weight for GENECOUNTINGpgc
Plot haplotype frequencies versus haplotype score statisticsplot.hap.score
Print a hap.score objectprint.hap.score
P value for a normal deviatepvalue
Quantile-comparison plotsqqfun
Q-Q plot for uniformly distributed random variableqqunif
2D QTL plotqtl2dplot
2D QTL plotlyqtl2dplotly
3D QTL plotqtl3dplotly
A QTL cis/trans classifierqtlClassifier
Distance-based signal identificationqtlFinder
A utility function to read ms outputread.ms.output
A function to read GRM fileReadGRM
A function to read GRM binary filesReadGRMBin
Allele on the reverse strandrevStrand
Start shinygaprunshinygap
Statistics for 2 by K tables2k
Sentinel identification from GWAS summary statisticssentinels
Functions for single nucleotide polymorphismsPARn snpHWE snpPAR snpPVE
A utility to generate SNPTEST sample filesnptest_sample
Power calculation for two-stage case-control designtscc
Whittemore-Halpern scores for allele-sharingwhscore
A function to write GRM fileWriteGRM
A function to write GRM binary fileWriteGRMBin
Conversion of chromosome names to stringsxy