From d24837b51dea172f94b96703da7c6e1ec4d0434c Mon Sep 17 00:00:00 2001 From: gaynorr Date: Fri, 1 Nov 2024 18:54:09 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20gaynorr/?= =?UTF-8?q?AlphaSimR@a171cf6089a828f03d24111f8f4d8f0d2ed67363=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 4 +- LICENSE-text.html | 4 +- articles/AlphaSimR.html | 8 +-- articles/DataImport.html | 8 +-- articles/Genome.html | 8 +-- articles/GenomicSelection.html | 8 +-- articles/Meiosis.html | 8 +-- articles/Misc.html | 8 +-- articles/QuantGen.html | 8 +-- articles/Traits.html | 8 +-- articles/index.html | 4 +- articles/intro.html | 8 +-- articles/traits.html | 8 +-- authors.html | 6 +- index.html | 4 +- news/index.html | 10 ++- pkgdown.js | 8 +++ pkgdown.yml | 4 +- reference/AlphaSimR-package.html | 6 +- reference/HybridPop-class.html | 6 +- reference/LociMap-class.html | 6 +- reference/MapPop-class.html | 6 +- reference/MultiPop-class.html | 6 +- reference/NamedMapPop-class.html | 6 +- reference/Pop-class.html | 9 +-- reference/RRBLUP.html | 6 +- reference/RRBLUP2.html | 6 +- reference/RRBLUPMemUse.html | 6 +- reference/RRBLUP_D.html | 6 +- reference/RRBLUP_D2.html | 6 +- reference/RRBLUP_GCA.html | 6 +- reference/RRBLUP_GCA2.html | 6 +- reference/RRBLUP_SCA.html | 6 +- reference/RRBLUP_SCA2.html | 6 +- reference/RRsol-class.html | 6 +- reference/RawPop-class.html | 6 +- reference/SimParam.html | 6 +- reference/TraitA-class.html | 6 +- reference/TraitA2-class.html | 6 +- reference/TraitA2D-class.html | 6 +- reference/TraitAD-class.html | 6 +- reference/TraitADE-class.html | 6 +- reference/TraitADEG-class.html | 6 +- reference/TraitADG-class.html | 6 +- reference/TraitAE-class.html | 6 +- reference/TraitAEG-class.html | 6 +- reference/TraitAG-class.html | 6 +- reference/aa.html | 6 +- reference/addSegSite.html | 6 +- reference/attrition.html | 6 +- reference/bv.html | 6 +- reference/cChr.html | 6 +- reference/calcGCA.html | 6 +- reference/dd.html | 6 +- reference/dot-newPop.html | 6 +- reference/doubleGenome.html | 6 +- reference/ebv.html | 6 +- reference/editGenome.html | 6 +- reference/editGenomeTopQtl.html | 6 +- reference/fastRRBLUP.html | 6 +- reference/genParam.html | 6 +- reference/genicVarA.html | 6 +- reference/genicVarAA.html | 6 +- reference/genicVarD.html | 6 +- reference/genicVarG.html | 6 +- reference/getGenMap.html | 6 +- reference/getNumThreads.html | 6 +- reference/getPed.html | 6 +- reference/getQtlMap.html | 6 +- reference/getSnpMap.html | 6 +- reference/gv.html | 6 +- reference/hybridCross.html | 6 +- reference/importGenMap.html | 6 +- reference/importHaplo.html | 6 +- reference/importInbredGeno.html | 6 +- reference/index.html | 4 +- reference/isFemale.html | 14 ++--- reference/isPop.html | 6 +- reference/makeCross.html | 6 +- reference/makeCross2.html | 6 +- reference/makeDH.html | 6 +- reference/mapLoci.html | 102 +++++++++++++++++++++++++++++++ reference/meanEBV.html | 6 +- reference/meanG.html | 6 +- reference/meanP.html | 6 +- reference/mergeGenome.html | 6 +- reference/mergePops.html | 6 +- reference/mutate.html | 6 +- reference/nInd.html | 6 +- reference/newEmptyPop.html | 6 +- reference/newMapPop.html | 6 +- reference/newMultiPop.html | 6 +- reference/newPop.html | 6 +- reference/pedigreeCross.html | 6 +- reference/pheno.html | 6 +- reference/popVar.html | 6 +- reference/pullIbdHaplo.html | 6 +- reference/pullMarkerGeno.html | 6 +- reference/pullMarkerHaplo.html | 6 +- reference/pullQtlGeno.html | 6 +- reference/pullQtlHaplo.html | 6 +- reference/pullSegSiteGeno.html | 6 +- reference/pullSegSiteHaplo.html | 6 +- reference/pullSnpGeno.html | 6 +- reference/pullSnpHaplo.html | 6 +- reference/quickHaplo.html | 6 +- reference/randCross.html | 6 +- reference/randCross2.html | 6 +- reference/reduceGenome.html | 6 +- reference/resetPop.html | 6 +- reference/runMacs.html | 39 +++--------- reference/runMacs2.html | 20 +++--- reference/sampleHaplo.html | 6 +- reference/selIndex.html | 6 +- reference/selInt.html | 6 +- reference/selectCross.html | 6 +- reference/selectFam.html | 6 +- reference/selectInd.html | 6 +- reference/selectOP.html | 6 +- reference/selectWithinFam.html | 6 +- reference/self.html | 6 +- reference/setEBV.html | 6 +- reference/setMarkerHaplo.html | 6 +- reference/setPheno.html | 6 +- reference/setPhenoGCA.html | 6 +- reference/setPhenoProgTest.html | 6 +- reference/smithHazel.html | 6 +- reference/solveMKM.html | 6 +- reference/solveMVM.html | 6 +- reference/solveRRBLUP.html | 6 +- reference/solveRRBLUPMK.html | 6 +- reference/solveRRBLUPMV.html | 6 +- reference/solveRRBLUP_EM.html | 6 +- reference/solveRRBLUP_EM2.html | 6 +- reference/solveRRBLUP_EM3.html | 6 +- reference/solveUVM.html | 6 +- reference/transMat.html | 6 +- reference/usefulness.html | 6 +- reference/varA.html | 6 +- reference/varAA.html | 6 +- reference/varD.html | 6 +- reference/varEBV.html | 6 +- reference/varG.html | 6 +- reference/varP.html | 6 +- reference/writePlink.html | 6 +- reference/writeRecords.html | 6 +- search.json | 2 +- sitemap.xml | 1 + 148 files changed, 568 insertions(+), 479 deletions(-) create mode 100644 reference/mapLoci.html diff --git a/404.html b/404.html index 55d1613a..038335a9 100644 --- a/404.html +++ b/404.html @@ -20,7 +20,7 @@ AlphaSimR - 1.6.0 + 1.6.1 + + + + + +
+
+
+ +

Finds positions of loci by marker name

+ Source: R/pullGeno.R +
mapLoci.Rd
+
+ +
+

Used to generate lociPerChr and lociLoc +objects for a set of markers. These objects can be passed +other functions for pulling genotypes or haplotypes.

+
+ +
+

Usage

+ 
mapLoci(markers, genMap)
+
+ +
+

Arguments

+ + +
markers
+

a vector of marker names

+ + +
genMap
+

a genetic map in AlphaSimR's internal +genetic map format

+ +
+
+

Value

+

A list containing lociPerChr and lociLoc +that can be

+
+ +
+ + +
+

Developed by Chris Gaynor.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + diff --git a/reference/meanEBV.html b/reference/meanEBV.html index fd68ef98..dec3a5d5 100644 --- a/reference/meanEBV.html +++ b/reference/meanEBV.html @@ -7,7 +7,7 @@ AlphaSimR - 1.6.0 + 1.6.1