Package: ASMap 1.0-8

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).

Authors:Julian Taylor [aut, cre], David Butler. [aut]

ASMap_1.0-8.tar.gz
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ASMap.pdf |ASMap.html✨
ASMap/json (API)
NEWS

# Install 'ASMap' in R:
install.packages('ASMap', repos = c('https://drj001.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/drj001/asmap/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • 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 population
  • mapDHf - An unconstructed marker set for a doubled haploid wheat population
  • mapF2 - Simulated constructed linkage map for a self pollinated F2 barley population

On CRAN:

6.48 score 1 stars 76 scripts 683 downloads 36 mentions 20 exports 10 dependencies

Last updated 2 days agofrom:6971607f5f. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-win-x86_64OKNov 05 2024
R-4.5-linux-x86_64OKNov 05 2024
R-4.4-win-x86_64OKNov 05 2024
R-4.4-mac-x86_64OKNov 05 2024
R-4.4-mac-aarch64OKNov 05 2024
R-4.3-win-x86_64OKNov 05 2024
R-4.3-mac-x86_64OKNov 05 2024
R-4.3-mac-aarch64OKNov 05 2024

Exports:alignCrossbreakCrosscombineMapfixClonesgenClonesheatMapmergeCrossmstmapmstmap.crossmstmap.data.framepp.initprofileGenprofileMarkpullCrosspushCrosspValuequickEststatGenstatMarksubsetCross

Dependencies:dotCall64fieldsgtoolslatticemapsqtlRColorBrewerRcppspamviridisLite

Efficient linkage map construction using R/ASMap

Rendered fromasmapvignette.Rnwusingknitr::knitron Nov 05 2024.

Last update: 2023-02-03
Started: 2023-02-02

Readme and manuals

Help Manual

Help pageTopics
Additional functions for linkage map construction and manipulation of R/qtl objects.ASMap-package
Graphical linkage group identity and alignment.alignCross
Break linkage groups of an 'qtl' cross objectbreakCross
Combine linkage maps from multiple 'qtl' cross objectscombineMap
Consensus genotypes for clonal genotype groupsfixClones
Find and report genotype clonesgenClones
Heat map of the estimated pairwise recombination fractions and LOD linkage between markers.heatMap
A constructed linkage map for a backcross barley populationmapBC
An unconstructed marker set for a backcross barley populationmapBCu
A constructed linkage map for a doubled haploid wheat populationmapDH
An unconstructed marker set for a doubled haploid wheat populationmapDHf
Simulated constructed linkage map for a self pollinated F2 barley populationmapF2
Merge linkage groups of an 'qtl' cross objectmergeCross
Extremely fast linkage map construction for 'qtl' objects using MSTmap.mstmap mstmap.cross
Extremely fast linkage map construction for data frame objects using MSTmap.mstmap.data.frame
Parameter initialization functionpp.init
Profile individual genotype statistics for an R/qtl cross objectprofileGen
Profile individual marker and interval statistics for an R/qtl cross objectprofileMark
Pull markers from a linkage map.pullCross
Push markers into an established R/qtl linkage map.pushCross
P-value graphpValue
Very quick estimation of genetic map distances.quickEst
Individual genotype statistics for an R/qtl cross objectstatGen
Individual marker and interval statistics for an R/qtl cross objectstatMark
Subset an R/qtl objectsubsetCross