gpmap: Analysing and plotting genotype-phenotype maps

This package contains tools for studying genotype-phenotype (GP) maps for bi-allelic loci underlying quantitative phenotypes. The 0.1 version is released in connection with the publication of Gjuvsland et al. (2003) and implements basic line plots and the monotonicity measures for GP maps presented in the paper. Reference: Gjuvsland AB, Wang Y, Plahte E and Omholt SW (2013) Monotonicity is a key feature of genotype-phenotype maps. Front. Genet. 4:216. doi: 10.3389/fgene.2013.00216 [\href{http://www.frontiersin.org/Journal/10.3389/fgene.2013.00216/full}{link}]

Author
Arne B. Gjuvsland <arne.gjuvsland@nmbu.no> and Yunpeng Wang <yunpeng.wng@gmail.com>
Date of publication
2014-01-09 12:30:26
Maintainer
Arne B. Gjuvsland <arne.gjuvsland@nmbu.no>
License
GPL-3
Version
0.1.1

View on CRAN

Man pages

decompose_monotone
Decompose genotype-phenotype map(s) using monotone regression
degree_of_monotonicity
Degree of monotonicity of GP map
enumerate_genotypes
Function for enumerating genotypes for N biallelic loci
generate_gpmap
Function for creating genotype-phenotype (GP) maps
gpmap-package
Tools for analysing and plotting genotype-phenotype maps
GPmaps
Dataset containing example GP maps
monotone_regression
Perform monotone regression on a genotype-phenotype (GP) map
partial_genotype_order
Generate partial ordering of genotype space based from allele...
plot.gpmap
Functions for creating lineplots of genotype-phenotype (GP)...
print.gpmap
Print function for 'gpmap' objects

Files in this package

gpmap
gpmap/tests
gpmap/tests/Examples
gpmap/tests/Examples/gpmap-Ex.Rout.save
gpmap/tests/test_code_example.Rout.save
gpmap/tests/test_code_example.R
gpmap/tests/genotype_test.R
gpmap/tests/genotype_test.Rout.save
gpmap/NAMESPACE
gpmap/data
gpmap/data/GPmaps.RData
gpmap/R
gpmap/R/genotypes.R
gpmap/R/gpmaps.R
gpmap/R/monotone_regression.R
gpmap/R/substitution_effects.R
gpmap/MD5
gpmap/DESCRIPTION
gpmap/man
gpmap/man/degree_of_monotonicity.Rd
gpmap/man/gpmap-package.Rd
gpmap/man/generate_gpmap.Rd
gpmap/man/enumerate_genotypes.Rd
gpmap/man/print.gpmap.Rd
gpmap/man/decompose_monotone.Rd
gpmap/man/GPmaps.Rd
gpmap/man/partial_genotype_order.Rd
gpmap/man/plot.gpmap.Rd
gpmap/man/monotone_regression.Rd