ASMap: Linkage Map Construction using the MSTmap Algorithm

Share:

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).

Author
Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler <david.butler@daff.qld.gov.au>.
Date of publication
2016-06-24 09:53:21
Maintainer
Julian Taylor <julian.taylor@adelaide.edu.au>
License
GPL (>= 2)
Version
0.4-7

View on CRAN

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

Files in this package

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