gpmap: Analysing and plotting genotype-phenotype maps
Version 0.1.1

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}]

Browse man pages Browse package API and functions Browse package files

Author Arne B. Gjuvsland <arne.gjuvsland@nmbu.no> and Yunpeng Wang <yunpeng.wng@gmail.com>
Date of publication2014-01-09 12:30:26
MaintainerArne B. Gjuvsland <arne.gjuvsland@nmbu.no>
LicenseGPL-3
Version0.1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("gpmap")

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

Functions

A Man page
AA Man page
AD Man page
D Man page
DA Man page
DD Man page
GPmaps Man page
decompose_monotone Man page Source code
decompose_monotone_single Man page Source code
degree_of_monotonicity Man page Source code
degree_of_monotonicity_single Man page Source code
enumerate_genotypes Man page Source code
generate_gpmap Man page Source code
gpmap Man page
gpmap-package Man page
monotone_regression Man page Source code
mouseweight Man page
partial_genotype_order Man page Source code
plot.gpmap Man page Source code
plot.gpmap.decomp.mono Man page
plot1_dec Source code
plot1_orig Source code
plot2_dec Source code
plot2_orig Source code
plot3_dec Source code
plot3_orig Source code
print.gpmap Man page Source code

Files

tests
tests/Examples
tests/Examples/gpmap-Ex.Rout.save
tests/test_code_example.Rout.save
tests/test_code_example.R
tests/genotype_test.R
tests/genotype_test.Rout.save
NAMESPACE
data
data/GPmaps.RData
R
R/genotypes.R
R/gpmaps.R
R/monotone_regression.R
R/substitution_effects.R
MD5
DESCRIPTION
man
man/degree_of_monotonicity.Rd
man/gpmap-package.Rd
man/generate_gpmap.Rd
man/enumerate_genotypes.Rd
man/print.gpmap.Rd
man/decompose_monotone.Rd
man/GPmaps.Rd
man/partial_genotype_order.Rd
man/plot.gpmap.Rd
man/monotone_regression.Rd
gpmap documentation built on May 19, 2017, 10:23 a.m.