Package: haplo.stats 1.9.5.1

haplo.stats: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.

Authors:Sinnwell JP, Schaid DJ

haplo.stats_1.9.5.1.tar.gz
haplo.stats_1.9.5.1.zip(r-4.5)haplo.stats_1.9.5.1.zip(r-4.4)haplo.stats_1.9.5.1.zip(r-4.3)
haplo.stats_1.9.5.1.tgz(r-4.4-x86_64)haplo.stats_1.9.5.1.tgz(r-4.4-arm64)haplo.stats_1.9.5.1.tgz(r-4.3-arm64)haplo.stats_1.9.5.1.tgz(r-4.3-x86_64)
haplo.stats_1.9.5.1.tar.gz(r-4.5-noble)haplo.stats_1.9.5.1.tar.gz(r-4.4-noble)
haplo.stats_1.9.5.1.tgz(r-4.4-emscripten)haplo.stats_1.9.5.1.tgz(r-4.3-emscripten)
haplo.stats.pdf |haplo.stats.html✨
haplo.stats/json (API)
NEWS

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

Peer review:

Datasets:
  • hapPower.demo - Set of haplotypes and frequencies for power and sample size calculations
  • hla.demo - HLA Loci and Serologic Response to Measles Vaccination
  • seqhap.dat - Simulated data for seqhap examples
  • seqhap.pos - Simulated data for seqhap examples

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

52 exports 2 stars 1.85 score 78 dependencies 6 dependents 94 scripts 1.1k downloads

Last updated 8 months agofrom:c51848a3a7. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 31 2024
R-4.5-win-x86_64OKAug 31 2024
R-4.5-linux-x86_64OKAug 31 2024
R-4.4-win-x86_64OKAug 31 2024
R-4.4-mac-x86_64OKAug 31 2024
R-4.4-mac-aarch64OKAug 31 2024
R-4.3-win-x86_64OKAug 01 2024
R-4.3-mac-aarch64OKAug 01 2024
R-4.3-mac-x86_64OKAug 01 2024

Exports:anova.haplo.glmfind.haplo.beta.qtfitted.haplo.glmgeno.count.pairsgeno1to2get.hapPairGinvhaplo.binomialhaplo.cchaplo.chistathaplo.designhaplo.emhaplo.em.controlhaplo.glmhaplo.glm.controlhaplo.grouphaplo.power.cchaplo.power.cc.ncphaplo.power.qthaplo.power.qt.ncphaplo.scanhaplo.scan.obshaplo.scan.simhaplo.scorehaplo.score.glmhaplo.score.mergehaplo.score.poddshaplo.score.slidelocator.haplolocusna.geno.keepplot.haplo.scoreplot.haplo.score.slideplot.seqhapprint.haplo.ccprint.haplo.emprint.haplo.glmprint.haplo.groupprint.haplo.scanprint.haplo.scoreprint.haplo.score.mergeprint.haplo.score.slideprint.seqhapprintBannerresiduals.haplo.glmscore.sim.controlseqhapsetupGenosummary.haplo.emsummary.haplo.glmsummaryGenovcov.haplo.glm

Dependencies:arsenalbackportsbase64encbslibcachemcheckmatecliclustercodetoolscolorspacedata.tabledigestevaluatefansifarverfastmapfontawesomeforeignFormulafsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmemoisemgcvmimemultcompmunsellmvtnormnlmennetpillarpkgconfigpolsplinequantregR6rappdirsRColorBrewerrlangrmarkdownrmsrpartrstudioapisandwichsassscalesSparseMstringistringrsurvivalTH.datatibbletinytexutf8vctrsviridisviridisLitewithrxfunyamlzoo

haplostats

Rendered fromhaplostats.Rnwusingutils::Sweaveon Aug 31 2024.

Last update: 2020-08-12
Started: 2020-08-12

Readme and manuals

Help Manual

Help pageTopics
Analysis of variance for haplo.glm model fitanova.haplo.glm anova.haplo.glmlist
Power and sample size for the chi-square distributionchisq.power chisq.power.dif chisq.sample.size
Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.dglm.fit haplo.binomial haplo.chistat haplo.enum haplo.score.glm haplo.score.podds mf.gindx residScaledGlmFit sr.class sr.class<- varfunc.glm.fit
Power and sample size for the F distributionf.power f.power.dif f.sample.size
Find beta coefficients for risk haplotypes, for specified r2find.beta.qt.phase.known find.haplo.beta.qt find.intercept.qt.phase.known
Fitted values from haplo.glm fitfitted.haplo.glm
Counts of Total Haplotype Pairs Produced by Genotypesgeno.count.pairs
convert genotype matrix from 1-column 2-columngeno1to2
Get a list of objects for haplotype pairsget.hapPair
Compute Generalized Inverse of Input MatrixGinv
Haplotype Association Analysis in a Case-Control designhaplo.cc
Build a design matrix for haplotypeshaplo.design
EM Computation of Haplotype Probabilities, with Progressive Insertion of Locihaplo.em
Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Locihaplo.em.control
Compute engine for haplotype EM algorithmhaplo.em.fitter
GLM Regression of Trait on Ambiguous Haplotypeshaplo.glm print.haplo.glm
Create list of control parameters for haplo.glmhaplo.glm.control
Frequencies for Haplotypes by Grouping Variablehaplo.group
Integer Rank Codes for Haplotypeshaplo.hash
Sets up a model frame for haplo.glmhaplo.model.frame
Compute either power or sample size for haplotype associations in a case-control study.find.intercept.logistic haplo.power.cc haplo.power.cc.ncp
Compute either power or sample size for haplotype associations with a quantitative trait.haplo.power.qt haplo.power.qt.ncp
Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the windowhaplo.scan haplo.scan.obs haplo.scan.sim
Score Statistics for Association of Traits with Haplotypeshaplo.score
Merge haplo.score And haplo.group Objectshaplo.score.merge
Score Statistics for Association of Traits with Haplotypeshaplo.score.slide
Set of haplotypes and frequencies for power and sample size calculationshapPower.demo
HLA Loci and Serologic Response to Measles Vaccinationhla.demo
Find Location from Mouse Clicks and Print Haplotypes on Plotlocator.haplo
Creates an object of class "locus"locus
Louis Information for haplo.glmlouis.info
Remove rows with NA in covariates, but keep genotypes with NAsna.geno.keep
Plot Haplotype Frequencies versus Haplotype Score Statisticsplot.haplo.score
Plot a haplo.score.slide Objectplot.haplo.score.slide
Plot a seqhap objectplot.seqhap
Print a haplo.cc objectprint.haplo.cc
Print contents of a haplo.em objectprint.haplo.em
Print a haplo.group objectprint.haplo.group
Print a haplo.scan objectprint.haplo.scan
Print a haplo.score objectprint.haplo.score
Print a haplo.score.merge objectprint.haplo.score.merge
Print the contents of a haplo.score.slide objectprint.haplo.score.slide
Print a nice bannerprintBanner
Accessing residuals for haplo.glm fitresiduals.haplo.glm
Create the list of control parameters for simulations in haplo.scorescore.sim.control
Sequential Haplotype Scan Association Analysis for Case-Control Dataprint.seqhap seqhap
Simulated data for seqhap examplesseqhap.dat seqhap.pos
Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.setupGeno
Summarize contents of a haplo.em objectsummary.haplo.em
Print and summary of a haplo.glm objectprint.summary.haplo.glm summary.haplo.glm
Summarize Full Haplotype Enumeration on Genotype MatrixsummaryGeno
variance-covariance matrix of a fitted haplo.glm objectvcov.haplo.glm
consistency checks for x.linked locusx.sexcheck