1. Introduction | 2. Installation | 3. Data loading | 4. Haplotype selection within small regions | 4.1 Creating haplotype data | 4.2 Selecting haplotypes | 5. Haplotype selection for large regions | References
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:
HTRX_1.2.4.tar.gz
HTRX_1.2.4.tar.gz(r-4.7-any)HTRX_1.2.4.tar.gz(r-4.6-any)
HTRX_1.2.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HTRX/json (API)
| # Install 'HTRX' in R: |
| install.packages('HTRX', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- example_data_nosnp - Example covariate data
- example_hap1 - Example genotype data for the first genome
- example_hap2 - Example genotype data for the second genome
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:79df34a6d8. Checks:2 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 201 | ||
| source / vignettes | OK | 254 | ||
| linux-release-x86_64 | NOTE | 165 | ||
| wasm-release | OK | 141 |
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:base64encBHbigmemorybigmemory.sribslibcachemcaretclasscliclockcodetoolscpp11data.tablediagramdialsDiceDesigndigestdplyre1071evaluatefarverfastglmfastmapfontawesomeforeachFormulafsfurrrfuturefuture.applyGauProgenericsggplot2glmnetglobalsgluegowergtablehardhathighrhtmltoolsipredisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelavalbfgslifecyclelistenvlubridatemagrittrMASSMatrixmemoisemimemixoptmodelenvModelMetricsnlmennetnumDerivparallellyparsnippillarpkgconfigplyrprettyunitspROCprodlimprogressrproxypurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrecipesreshape2rlangrmarkdownrpartrsampleS7sassscalessfdshapeslidersparsevctrssplitfngrSQUAREMstringistringrsurvivaltailortibbletidyrtidyselecttimechangetimeDatetinytextunetzdbutf8uuidvctrsviridisLitewarpwithrworkflowsxfunyamlyardstick
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| HTRX: Haplotype Trend Regression with eXtra flexibility | HTRX-package HTRX |
| Compute variance explained by models | computeR2 mypredict |
| Data split | data_split kfold_split twofold_split |
| Cumulative HTRX on long haplotypes | do_cumulative_htrx do_cumulative_htrx_step1 extend_haps make_cumulative_htrx |
| Two-stage HTRX: Model selection on short haplotypes | do_cv do_cv_step1 infer_fixedfeatures infer_step1 |
| Direct HTRX: k-fold cross-validation on short haplotypes | do_cv_direct |
| Example covariate data | example_data_nosnp |
| Example genotype data for the first genome | example_hap1 |
| Example genotype data for the second genome | example_hap2 |
| Maximum independent features for HTRX | htrx_max |
| Total number of features for HTRX | htrx_nfeatures |
| Generate haplotype data | make_htr make_htrx make_snp |
| Model fitting | themodel |