ASMap: Linkage Map Construction using the MSTmap Algorithm
Version 0.4-7

Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).

Browse man pages Browse package API and functions Browse package files

AuthorJulian Taylor <julian.taylor@adelaide.edu.au>, David Butler <david.butler@daff.qld.gov.au>.
Date of publication2016-06-24 09:53:21
MaintainerJulian Taylor <julian.taylor@adelaide.edu.au>
LicenseGPL (>= 2)
Version0.4-7
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ASMap")

Man pages

alignCross: Graphical linkage group identity and alignment.
ASMap-internal: Internal fastMap functions
ASMap-package: Additional functions for linkage map construction and...
breakCross: Break linkage groups of an R/qtl cross object
combineMap: Combine linkage maps from multiple R/qtl cross objects
fixClones: Consensus genotypes for clonal genotype groups
genClones: Find and report genotype clones
heatMap: Heat map of the estimated pairwise recombination fractions...
mapBC: A constructed linkage map for a backcross barley population
mapBCu: An unconstructed marker set for a backcross barley population
mapDH: A constructed linkage map for a doubled haploid wheat...
mapDHf: An unconstructed marker set for a doubled haploid wheat...
mapF2: Simulated constructed linkage map for a self pollinated F2...
mergeCross: Merge linkage groups of an R/qtl cross object
mstmap.cross: Extremely fast linkage map construction for R/qtl objects...
mstmap.data.frame: Extremely fast linkage map construction for data frame...
pp.init: Parameter initialization function
profileGen: Profile individual genotype statistics for an R/qtl cross...
profileMark: Profile individual marker and interval statistics for an...
pullCross: Pull markers from a linkage map.
pushCross: Push markers into an established R/qtl linkage map.
quickEst: Very quick estimation of genetic map distances.
statGen: Individual genotype statistics for an R/qtl cross object
statMark: Individual marker and interval statistics for an R/qtl cross...
subsetCross: Subset an R/qtl object

Functions

ASMap-package Man page
alignCross Man page Source code
breakCross Man page Source code
combineMap Man page Source code
fixClones Man page Source code
genClones Man page Source code
heatMap Man page Source code
mapBC Man page
mapBCu Man page
mapDH Man page
mapDHf Man page
mapF2 Man page
mergeCross Man page Source code
mstmap Man page Source code
mstmap.cross Man page Source code
mstmap.data.frame Man page Source code
mstmap.default Man page Source code
pp.init Man page Source code
profileGen Man page Source code
profileMark Man page Source code
pullCross Man page Source code
pushCross Man page Source code
quickEst Man page Source code
statGen Man page Source code
statMark Man page Source code
subsetCross Man page Source code

Files

inst
inst/NEWS.Rd
inst/doc
inst/doc/asmapvignette.R
inst/doc/asmapvignette.Rnw
inst/doc/asmapvignette.pdf
src
src/linkage_group_DH.cpp
src/sexp.cpp
src/constants.h
src/mst.cpp
src/is_number.cpp
src/MSTOpt.cpp
src/linkage_group_DH.h
src/genetic_map_DH.cpp
src/linkage_group_RIL.h
src/linkage_group_RIL.cpp
src/MSTOpt.h
src/genetic_map_RIL.h
src/genetic_map_DH.h
src/genetic_map_RIL.cpp
NAMESPACE
data
data/mapDHf.RData
data/mapBC.RData
data/mapDH.RData
data/mapF2.RData
data/mapBCu.RData
R
R/mstmap11.R
vignettes
vignettes/biometrika.bst
vignettes/heatmap.png
vignettes/asmapvignette.Rnw
vignettes/SAGI.sty
vignettes/SAGI.png
vignettes/pval.pdf
vignettes/missBC4.png
vignettes/ref.bib
vignettes/plotrfDH.png
vignettes/GRDC_LOGO_2015_inline.png
vignettes/missBCu.png
vignettes/heatmapDH.png
vignettes/UoA.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/ASMap-internal.Rd
man/pullCross.Rd
man/pushCross.Rd
man/combineMap.Rd
man/mapBCu.Rd
man/mapDH.Rd
man/mapF2.Rd
man/alignCross.Rd
man/mapDHf.Rd
man/pp.init.Rd
man/mergeCross.Rd
man/mstmap.data.frame.Rd
man/statMark.Rd
man/profileMark.Rd
man/mstmap.cross.Rd
man/genClones.Rd
man/fixClones.Rd
man/breakCross.Rd
man/subsetCross.Rd
man/ASMap-package.Rd
man/profileGen.Rd
man/mapBC.Rd
man/quickEst.Rd
man/heatMap.Rd
man/statGen.Rd
ASMap documentation built on May 19, 2017, 3:27 p.m.