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J integrates R/qtl to perform quantitative trait locus (QTL) analysis of rodent mapping populations.

Key Features:

• R/qtl integration: Leverages R/qtl for statistical QTL analyses including scanning and regression-based modeling.
• Java-based implementation: Implements analysis workflows in Java while interfacing with R/qtl computational routines.
• Data formatting: Prepares datasets into formats compatible with R/qtl for downstream analysis.
• Data quality control: Performs quality-control checks on input genotype and phenotype data.
• Main-scan QTL analysis: Conducts main-scan analyses to identify primary genomic regions associated with phenotypic traits.
• Pair-scan QTL analysis: Performs pairwise locus scans to examine interactions and detect epistatic effects.
• Multiple regression modeling: Applies multiple regression approaches to assess the combined influence of multiple loci on traits.
• Rodent cross support: Supports analysis workflows tailored to rodent mapping population data.

Scientific Applications:

• Genetic mapping in rodents: Mapping genomic regions that influence quantitative phenotypes in rodent crosses.
• Epistasis detection: Identifying pairwise locus interactions and epistatic effects using pair-scan analyses.
• Multigenic trait modeling: Modeling the contributions of multiple genetic factors to phenotypic variation via multiple regression.

Methodology:

Integration with R/qtl to perform data preparation, data quality control, main-scan and pair-scan QTL analyses, and multiple regression modeling.