HTRX: an R package for learning non-contiguous haplotypes associated with a phenotype

Abstract

AbstractSummaryHaplotype Trend Regression with eXtra flexibility (HTRX) is an R package which uses cross-validation to learn sets of interacting features for a prediction. HTRX identifies haplotypes composed of non-contiguous single nucleotide polymorphisms (SNPs) associated with a phenotype. To reduce the space and computational complexity when investigating many features, we constrain the search by growing good feature sets using ‘Cumulative HTRX’, and limit the maximum complexity of a feature set.AvailabilityHTRX is implemented in R and is available under GPL-3 license from CRAN and Github at:https://github.com/YaolingYang/HTRX.Contactyaoling.yang@bristol.ac.uk