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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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ASMap/json (API)

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

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:

Conda:

cpp

5.38 score 3 stars 80 scripts 828 downloads 36 mentions 20 exports 10 dependencies

Last updated from:6971607f5f. Checks:11 WARNING, 1 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING126
linux-devel-x86_64WARNING284
source / vignettesERROR371
linux-release-arm64WARNING132
linux-release-x86_64WARNING122
macos-release-arm64WARNING114
macos-release-x86_64WARNING215
macos-oldrel-arm64WARNING101
macos-oldrel-x86_64WARNING184
windows-develWARNING136
windows-releaseWARNING109
windows-oldrelWARNING116
wasm-releaseOK102

Exports:alignCrossbreakCrosscombineMapfixClonesgenClonesheatMapmergeCrossmstmapmstmap.crossmstmap.data.framepp.initprofileGenprofileMarkpullCrosspushCrosspValuequickEststatGenstatMarksubsetCross

Dependencies:dotCall64fieldsgtoolslatticemapsqtlRColorBrewerRcppspamviridisLite

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