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'))

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.

2.70 score 5 scripts 209 downloads 19 exports 98 dependencies

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

Target	Result	Date
Doc / Vignettes	OK	Dec 06 2024
R-4.5-linux	NOTE	Dec 06 2024

Exports:computeR2 do_cumulative_htrx do_cumulative_htrx_step1 do_cv do_cv_direct do_cv_step1 extend_haps htrx_max htrx_nfeatures infer_fixedfeatures infer_step1 kfold_split make_cumulative_htrx make_htr make_htrx make_snp mypredict themodel twofold_split

Dependencies:BH bigmemory bigmemory.sri caret class cli clock codetools colorspace cpp11 data.table diagram dials DiceDesign digest doFuture dplyr e1071 fansi farver fastglm foreach furrr future future.apply generics ggplot2 glmnet globals glue gower GPfit gtable hardhat ipred isoband iterators KernSmooth labeling lattice lava lhs lifecycle listenv lubridate magrittr MASS Matrix mgcv modelenv ModelMetrics munsell nlme nnet numDeriv parallelly parsnip pillar pkgconfig plyr prettyunits pROC prodlim progressr proxy purrr R6 RColorBrewer Rcpp RcppEigen recipes reshape2 rlang rpart rsample scales sfd shape slider SQUAREM stringi stringr survival tibble tidyr tidyselect timechange timeDate tune tzdb utf8 uuid vctrs viridisLite warp withr workflows yardstick

HTRX: an R package for learning non-contiguous haplotypes

Yaoling Yang, Daniel Lawson

Rendered fromHTRX_vignette.Rmdusingknitr::rmarkdownon Dec 06 2024.

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

Citation

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