Package: HTRX 1.2.4

Yaoling Yang

HTRX: Haplotype Trend Regression with eXtra Flexibility (HTRX)

Detection of haplotype patterns that include single nucleotide polymorphisms (SNPs) and non-contiguous haplotypes that are associated with a phenotype. Methods for implementing HTRX are described in Yang Y, Lawson DJ (2023) <doi:10.1093/bioadv/vbad038> and Barrie W, Yang Y, Irving-Pease E.K, et al (2024) <doi:10.1038/s41586-023-06618-z>.

Authors:Yaoling Yang [aut, cre], Daniel Lawson [aut]

HTRX_1.2.4.tar.gz
HTRX_1.2.4.tar.gz(r-4.5-noble)HTRX_1.2.4.tar.gz(r-4.4-noble)
HTRX_1.2.4.tgz(r-4.4-emscripten)HTRX_1.2.4.tgz(r-4.3-emscripten)
HTRX.pdf |HTRX.html
HTRX/json (API)

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

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

2.70 score 5 scripts 181 downloads 19 exports 98 dependencies

Last updated 10 months agofrom:79df34a6d8. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 06 2024
R-4.5-linuxNOTENov 06 2024

Exports:computeR2do_cumulative_htrxdo_cumulative_htrx_step1do_cvdo_cv_directdo_cv_step1extend_hapshtrx_maxhtrx_nfeaturesinfer_fixedfeaturesinfer_step1kfold_splitmake_cumulative_htrxmake_htrmake_htrxmake_snpmypredictthemodeltwofold_split

Dependencies:BHbigmemorybigmemory.sricaretclasscliclockcodetoolscolorspacecpp11data.tablediagramdialsDiceDesigndigestdoFuturedplyre1071fansifarverfastglmforeachfurrrfuturefuture.applygenericsggplot2glmnetglobalsgluegowerGPfitgtablehardhatipredisobanditeratorsKernSmoothlabelinglatticelavalhslifecyclelistenvlubridatemagrittrMASSMatrixmgcvmodelenvModelMetricsmunsellnlmennetnumDerivparallellyparsnippillarpkgconfigplyrprettyunitspROCprodlimprogressrproxypurrrR6RColorBrewerRcppRcppEigenrecipesreshape2rlangrpartrsamplescalessfdshapesliderSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetunetzdbutf8uuidvctrsviridisLitewarpwithrworkflowsyardstick

HTRX: an R package for learning non-contiguous haplotypes

Rendered fromHTRX_vignette.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-02-10
Started: 2023-02-14

Readme and manuals

Help Manual

Help pageTopics
HTRX: Haplotype Trend Regression with eXtra flexibilityHTRX-package HTRX
Compute variance explained by modelscomputeR2 mypredict
Data splitdata_split kfold_split twofold_split
Cumulative HTRX on long haplotypesdo_cumulative_htrx do_cumulative_htrx_step1 extend_haps make_cumulative_htrx
Two-stage HTRX: Model selection on short haplotypesdo_cv do_cv_step1 infer_fixedfeatures infer_step1
Direct HTRX: k-fold cross-validation on short haplotypesdo_cv_direct
Example covariate dataexample_data_nosnp
Example genotype data for the first genomeexample_hap1
Example genotype data for the second genomeexample_hap2
Maximum independent features for HTRXhtrx_max
Total number of features for HTRXhtrx_nfeatures
Generate haplotype datamake_htr make_htrx make_snp
Model fittingthemodel