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

Functions

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

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

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