Initial commit

.gitignore

@@ -0,0 +1,10 @@
+*.aux
+*.bbl
+*.blg
+*.log
+*~
+.Rhistory
+.RData
+*.pdf
+*.RData
+*.Rout

Makefile

@@ -0,0 +1,22 @@
+pdf: ailprob.pdf Revised/response.pdf
+
+all: pdf
+
+ailprob.pdf: ailprob.tex ailprob.bib genetics.bst Figs/fig1.eps
+	pdflatex ailprob
+	bibtex ailprob
+	pdflatex ailprob
+	pdflatex ailprob
+	pdflatex ailprob
+
+Figs/fig1.pdf: R/R_fig.R 
+	cd R;R CMD BATCH '--args eps=FALSE' R_fig.R
+
+Figs/fig1.eps: R/R_fig.R 
+	cd R;R CMD BATCH '--args eps=TRUE' R_fig.R
+
+clean: 
+	\rm -f *.aux *.bbl *.blg *.log *.bak *~ *.Rout */*~ */*.Rout */*.aux */*.log
+
+cleanall: 
+	\rm -f *.aux *.bbl *.blg *.log *.pdf *.bak *~ *.Rout */*~ */*.Rout */*.pdf */*.aux */*.log

ailprob.bib

@@ -0,0 +1,247 @@
+
+@article{Haley1992,
+	Author = {C. S. Haley and S. A. Knott},
+	Journal = {Heredity},
+	Number = {4},
+	Pages = {315--324},
+	Title = {A simple regression method for mapping quantitative trait loci in line crosses using flanking markers},
+	Volume = {69},
+	Year = {1992}}
+
+@article{Lander1989,
+	Author = {E. S. Lander and D. Botstein},
+	Journal = {Genetics},
+	Number = {1},
+	Pages = {185--199},
+	Title = {Mapping {M}endelian factors underlying quantitative traits using {RFLP} linkage maps},
+	Volume = {121},
+	Year = {1989}}
+
+@Manual{R,
+       title        = {R: A Language and Environment for Statistical
+                       Computing},
+       author       = {{R Development Core Team}},
+       organization = {R Foundation for Statistical Computing},
+       address      = {Vienna, Austria},
+       year         = 2010,
+       note         = {{ISBN} 3-900051-07-0},
+       url          = {http://www.R-project.org}
+     }
+
+@Manual{Maxima,
+title = {Maxima, a computer algebra system, version 5.24.0},
+author = {{Maxima Group}},
+year = {2011},
+url = {http://maxima.sourceforge.net/},
+address = {Sebastopol, CA}
+}
+                  
+@book{Perl,
+title = {Programming Perl},
+edition = {3rd},
+publisher = {O'Reilly Media},
+year = {2000},
+author = {Larry Wall and Tom Christiansen and Jon Orwant} }
+
+@article{Teuscher2007,
+author = {Teuscher, Friedrich and Broman, Karl W},
+journal = {Genetics},
+pages = {1267--1274},
+title = {Haplotype probabilities for multiple-strain recombinant inbred lines},
+volume = {175},
+year = {2007}
+}
+                  
+@article{Broman2005,
+author = {Broman, K. W.},
+journal = {Genetics},
+pages = {1133--1146},
+title = {The genomes of recombinant inbred lines},
+volume = {169},
+year = {2005}
+}
+
+@article{Kimura1963,
+author = {Kimura, Motoo},
+journal = {Biometrics},
+pages = {1--17},
+title = {A probability method for treating inbreeding systems, especially with linked genes},
+volume = {19},
+year = {1963}
+}
+
+@article{CTC2004,
+author = {{Complex Trait Consortium}},
+journal = {Nat. Genet.},
+pages = {1133--1137},
+title = {The {C}ollaborative {C}ross, a community resource for the genetic analysis of complex traits},
+volume = {36},
+year = {2004}
+}
+
+@article{Haldane1931,
+author = {Haldane, J B S and Waddington, C H},
+journal = {Genetics},
+pages = {357--374},
+title = {Inbreeding and linkage},
+volume = {16},
+year = {1931}
+}
+
+
+@article{Macdonald2007,
+author = {Macdonald, Stuart J and Long, Anthony D},
+journal = {Genetics},
+pages = {1261--1281},
+title = {{Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster}},
+volume = {176},
+year = {2007}
+}
+
+@article{Kover2009,
+author = {Kover, Paula X and Valdar, William and Trakalo, Joseph and Scarcelli, Nora and Ehrenreich, Ian M and Purugganan, Michael D and Durrant, Caroline and Mott, Richard},
+journal = {{PLoS} {G}enet.},
+pages = {e1000551},
+title = {{A multiparent advanced generation inter-cross to fine-map quantitative traits in \emph{Arabidopsis thaliana}}},
+volume = {5},
+year = {2009}
+}
+
+@article{Cavanagh2008,
+author = {Cavanagh, Colin and Morell, Matthew and Mackay, Ian and Powell, Wayne},
+journal = {Curr. Opin. Plant Biol.},
+pages = {215--221},
+title = {{From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants}},
+volume = {11},
+year = {2008}
+}
+
+@article{Aylor2011,
+author = {Aylor, David L. and Valdar, William and Foulds-Mathes, Wendy and Buus, Ryan J. and Verdugo, Ricardo A. and Baric, Ralph S. and Ferris, Martin T. and Frelinger, Jeff A. and Heise, Mark and Frieman, Matt B. and Gralinski, Lisa E. and Bell, Timothy A. and Didion, John D. and Hua, Kunjie and Nehrenberg, Derrick L. and Powell, Christine L. and Steigerwalt, Jill and Xie, Yuying and Kelada, Samir N. P. and Collins, Francis S. and Yang, Ivana V. and Schwartz, David A. and Branstetter, Lisa A. and Chesler, Elissa J. and Miller, Darla R. and Spence, Jason and Liu, Eric Yi and Mcmillan, Leonard and Sarkar, Abhishek and Wang, Jeremy and Wang, Wei and Zhang, Qi and Broman, Karl W. and Korstanje, Ron and Durrant, Caroline and Mott, Richard and Iraqi, Fuad A. and Pomp, Daniel and Threadgill, David and Pardo-Manuel de Villena, Fernando and Churchill, Gary A.},
+journal = {Genome Res.},
+title = {Genetic analysis of complex traits in the emerging {C}ollaborative {C}ross},
+pages = {1213--1222},
+year = {2011},
+volume = {21}                 
+}
+
+@article{Burke1958,
+author = {Burke, C. J. and Rosenblatt, M.},
+journal = {Ann. Math. Stat.},
+pages = {1112--1122},
+title = {{A Markovian function of a Markov chain}},
+volume = {29},
+year = {1958}
+}
+
+@book{Graham1994,
+author = {Graham, Ronald L. and Knuth, Donald E. and Patashnik, Oren},
+title = {Concrete Mathematics},
+edition = {2nd},
+publisher = {Addison-Wesley},
+city = {Upper Saddle River, NJ},
+year = {1994} }
+
+@article{Svenson2012,
+author = {Svenson, Karen L. and Gatti, Daniel M. and Valdar, William and Welsh, Catherine E. and Cheng, Riyan and Chesler, Elissa J. and Palmer, Abraham A. and McMillan, Leonard and Churchill, Gary A.},
+title = {The mouse diversity outcross population},
+year = {2012},
+journal = {Genetics},
+volume = {in press [CC-CROSS CITATION CC12]}
+}
+
+@article{Broman2012,
+author = {Broman, K. W.},
+journal = {Genetics},
+title = {Genotype probabilities at intermediate generations in the construction of recombinant inbred lines},
+volume = {in press [CC-CROSS CITATION CC3]},
+year = {2012}
+}
+
+@article{Liu2010,
+author = {Liu, E. Y. and Zhang, Q. and McMillan, L. and de Villena, F. P. and  Wang,  W.},
+year = {2010},
+title = {Efficient genome ancestry inference in complex pedigrees with inbreeding},
+journal = {Bioinformatics},
+volume = {26},
+pages = {i199--i207} }
+
+@article{Mott2000,
+author = {Mott, Richard and Talbot, Christopher J and Turri, Maria G and Collins, Allan C and Flint, Jonathan},
+journal = {Proc. Natl. Acad. Sci. USA},
+pages = {12649--12654},
+title = {A method for fine mapping quantitative trait loci in outbred animal stocks},
+volume = {97},
+year = {2000}
+}
+
+@article{Darvasi1995,
+author = {Darvasi, A. and Soller, M.},
+journal = {Genetics},
+pages = {1199--1207},
+title = {Advanced intercross lines, an experimental population for fine genetic mapping},
+volume = {141},
+year = {1995}
+}
+
+@book{Bulmer1980,
+author = {Bulmer, M. G.},
+title = {The mathematical theory of quantitative genetics},
+publisher = {Claredon Press},
+location = {Oxford},
+year = {1980}
+}
+
+@book{Broman2009,
+author = {Broman, K. W. and Sen, \'S.},
+title = {A guide to {QTL} mapping with {R}/qtl},
+publisher = {Springer},
+location = {New York},
+year = {2009}
+}
+
+@article{Norgard2008,
+author = {Norgard, Elizabeth A and Roseman, Charles C and Fawcett, Gloria L and Pavlic, Mihaela and Morgan, Clinton D and Pletscher, L Susan and Wang, Bing and Cheverud, James M},
+journal = {J. Bone Miner. Res.},
+mendeley-tags = {2297},
+pages = {887--895},
+title = {identification of quantitative trait loci affecting murine long bone length in a two-generation intercross of {LG/J} and {SM/J} mice},
+volume = {23},
+year = {2008}
+}
+                  
+@article{Kelly2010,
+author = {Kelly, Scott A and Nehrenberg, Derrick L and Peirce, Jeremy L and Hua, Kunjie and Steffy, Brian M and Wiltshire, Tim and de Villena, Fernando Pardo-Manuel and {Garland, Theodore}, Jr. and Pomp, Daniel},
+journal = {Physiol. Genomics},
+pages = {190--200},
+title = {Genetic architecture of voluntary exercise in an advanced intercross line of mice},
+volume = {42},
+year = {2010}
+}
+
+@article{Broman2002,
+author = {Broman, K. W. and Rowe, L. B. and Churchill, G. A. and Paigen, Ken},
+journal = {Genetics},
+pages = {1123--1131},
+title = {Crossover interference in the mouse},
+volume = {160},
+year = {2002}
+}
+
+@article{Besnier2011,
+author = {Besnier, Francois and Wahlberg, Per and R\"{o}nneg\r{a}rd, Lars and Ek, Weronica and Andersson, Leif and Siegel, Paul B and Carlborg, Orjan},
+journal = {Genet. Sel. Evol.},
+pages = {3},
+title = {Fine mapping and replication of {QTL} in outbred chicken advanced intercross lines},
+volume = {43},
+year = {2011}
+}
+                  
+@article{PongWong2001,
+author = {Pong-Wong, Ricardo and George, Andrew Winston and Woolliams, James Arthur and Haley, Chris Simon},
+journal = {Genet. Sel. Evol.},
+pages = {453--471},
+title = {A simple and rapid method for calculating identity-by-descent matrices using multiple markers},
+volume = {33},
+year = {2001}
+}