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-4.5-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')) |
- 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 9 months agofrom:79df34a6d8. Checks:OK: 1 NOTE: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 06 2024 |
R-4.5-linux | NOTE | Nov 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
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 |