shapeQTL: shape QTL mapping experiment with R

Description Details Author(s) References Examples


Functions in this package allow one to perform statistical analyses to map quantitative trait locus for geometric morphometric data


Geometric morphometrics defines shape as a multivariate trait. Gene pleiotropy on landmark coordinates is the underlying genetic model by definition and multivariate methods are required to map QTL. The package provides Haley-Knott mapping for shape data derived from other R packages: geomorph, Morpho, Momocs or other open source softwares for geometric morphometrics : e.g., MorphoJ, and for genotype probabilities derived from specific packages depending on the type of crosses (for example calc.genoprob from R/qtl for inbred strains).


Nicolas Navarro [email protected]


Haley CS, Knott SA (1992). A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315<e2><80><93>324.

Knott SA, Haley CS (2000). Multitrait least squares for quantitative trait loci detection. Genetics 156: 899<e2><80><93>911.

Klingenberg CP, Leamy LJ, Routman EJ, Cheverud JM (2001). Genetic architecture of mandible shape in mice: effects of quantitative trait loci analyzed by geometric morphometrics. Genetics 157: 785<e2><80><93>802.

Klingenberg CP (2010). Evolution and development of shape: integrating quantitative approaches. Nature Reviews Genetics 11: 623<e2><80><93>635.

Maga AM, Navarro N, Cunningham ML, Cox TC (2015). Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico. Front Physiol 6: 1<e2><80><93>13.



nnavarro/shapeQTL documentation built on Sept. 29, 2017, 5:59 p.m.