ASMap: Linkage Map Construction using the MSTmap Algorithm

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).

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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.