README.md

In andrewparkermorgan/multiparental: An R package for visualization and analysis of haplotypes in experimental crosses

R/multiparental

An R package for exploring, visualising and analysing haplotype data from "multiparental populations", ie. populations arising from breeding schemes such as the Collaborative Cross, Diversity Outbred or Heterogeneous Stock in which the founder haplotypes are known. Currently it is mouse-centric but not mouse-specific; it could be used with eg. the MAGIC population in Arabidopsis.

The core data structure is built on the GenomicRanges::GRanges class, which supports fast overlap queries and other operations on genomic intervals (more generally, integer ranges.)

Due to unresolved issues around function exports from GenomicRanges, multiparental only works if GenomicRanges has also been loaded into the R environment.

Functions

• fast queries across large sets (>1000) of inferred haplotypes
• ggplot2-based plotting of genome mosaics
• haplotype-based QTL-mapping under several phenotype models

Interop

The package interacts with Karl Broman's R/qtl (http://www.rqtl.org) package for QTL-mapping, and my megamuga_hmm package (coming soon) for performing haplotype inference from dense genotypes.

TODO

• add case-control QTL-mapping (via 2xk contingency tables)
• break off visualisation functions into separate package (genomeviz)
• figure out dependency on GenomicRanges

andrewparkermorgan/multiparental documentation built on May 10, 2019, 11:09 a.m.