Package: haplo.ccs 1.3.2

Benjamin French

haplo.ccs: Estimate Haplotype Relative Risks in Case-Control Data

Haplotype and covariate relative risks in case-control data are estimated by weighted logistic regression. Diplotype probabilities, which are estimated by EM computation with progressive insertion of loci, are utilized as weights. French et al. (2006) <doi:10.1002/gepi.20161>.

Authors:Benjamin French[aut, cre], Thomas Lumley[aut, cre], Shawn Garbett[ctb]

haplo.ccs_1.3.2.tar.gz
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haplo.ccs.pdf |haplo.ccs.html✨
haplo.ccs/json (API)

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

Peer review:

Bug tracker:https://github.com/vubiostat/haplo.ccs/issues

Datasets:
  • age - Example Dataset for 'haplo.ccs'
  • case - Example Dataset for 'haplo.ccs'
  • gender - Example Dataset for 'haplo.ccs'
  • geno - Example Dataset for 'haplo.ccs'
  • race - Example Dataset for 'haplo.ccs'

On CRAN:

19 exports 0.73 score 79 dependencies 1 scripts 185 downloads

Last updated 2 years agofrom:914f17cf3d. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winOKSep 12 2024
R-4.5-linuxOKSep 12 2024
R-4.4-winOKSep 12 2024
R-4.4-macOKSep 12 2024
R-4.3-winOKAug 13 2024
R-4.3-macOKAug 13 2024

Exports:AIC.haplo.ccsanova.haplo.ccscoef.haplo.ccscount.hapsfitted.haplo.ccshaplohaplo.ccshaplo.ccs.fithaplo.freqhaplo.hpplogLik.haplo.ccsoneprint.haplo.ccsprint.summary.haplo.ccsresiduals.haplo.ccsreturn.hapssandcovsummary.haplo.ccsvcov.haplo.ccs

Dependencies:arsenalbackportsbase64encbslibcachemcheckmatecliclustercodetoolscolorspacedata.tabledigestevaluatefansifarverfastmapfontawesomeforeignFormulafsggplot2gluegridExtragtablehaplo.statshighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmemoisemgcvmimemultcompmunsellmvtnormnlmennetpillarpkgconfigpolsplinequantregR6rappdirsRColorBrewerrlangrmarkdownrmsrpartrstudioapisandwichsassscalesSparseMstringistringrsurvivalTH.datatibbletinytexutf8vctrsviridisviridisLitewithrxfunyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Specify an Allele Matrix, Inheritance Mode, and Grouping for Rare Haplotypeshaplo
Estimate Haplotype Relative Risks in Case-Control DataAIC.haplo.ccs anova.haplo.ccs coef.haplo.ccs count.haps fitted.haplo.ccs haplo.ccs haplo.ccs.fit haplo.freq logLik.haplo.ccs one print.haplo.ccs print.summary.haplo.ccs residuals.haplo.ccs return.haps summary.haplo.ccs vcov.haplo.ccs
Obtain Summaries of Phase Ambiguityhaplo.hpp
Example Dataset for 'haplo.ccs'age case gender geno race renin
Compute Sandwich Variance-Covariance Estimatessandcov