shapeQTL: shape QTL mapping experiment with R

Description Details Author(s) References Examples

Description

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

Details

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).

Author(s)

Nicolas Navarro [email protected]

References

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.

Examples

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