Version history of R genetic analysis package (R/gap) Version 1.1-3 06-12-2011 Revise gap.Rnw to be compatible with kinship_1.1.2 30-11-2011 Revise hwe.cc components and therefore NAMESPACE according to Wang, Li [li.wang@vanderbilt.edu] Suggest rms instead of Design in DESCRIPTIOIN and therefore modify hap.score.R 11-11-2011 Add examples of HWE for multiple markers as done for Roger Vallejo [Roger.Vallejo@ARS.USDA.GOV] 03-10-2011 Add url to twinan90 example and .png example for mhtplot 29-08-2011 Revise asplot to allow for is.na(RSQR) and add NCBI2R example 12-08-2011 Revise asplot as with the package vignette 09-06-2011 Activate ylab, according to Marcel den Hoed [marcel.denhoed@mrc-epid.cam.ac.uk] 03-06-2011 Replace snca.RData with PD.rda 31-05-2011 Refine mhtplot and documentation according to Franco, Luis Miguel [lfranco@bcm.edu] 04-05-2011 Tidy up some loose ends from Version 1.1-2 Version 1.1-2 03-05-2011 Modify package vignette after cross-check with package kinship 01-05-2011 Revise kin.morgan (finally) with bug-fix as reported by Lukas Keller [lukas.keller@ieu.uzh.ch] 14-04-2011 Add --resave-data option when running R CMD build Version 1.1-1 10-12-2010 Add into vignette results from pbsize/fbsize/ccsize and figures as produced by asplot, ESplot, mhtplot, and qqunif 25-11-2010 Add type argument to mht.control() so that it is appropriate for lod score analysis 23-11-2010 Clarify colors and hcolors in mhtplot 19-11-2010 Add /usr/share/texlive/texmf-dist/tex/latex/ltxmisc/a4wide.sty under Fedora 13 and Comment on \usepackage{a4wide/amsmath/epsfig} in gap.Rnw enable build/check Change some table() calls to unique in Mhtplot to keep genes in order Version 1.1-0 17-11-2010 Enable rotated ticks on the x-axis and retain cutoffs argument after HaemGenRBC plot 14-11-2010 Relocate highlight region in mhtplot after the usual data points 05-11-2010 Remove attach/detach data statements in mtdt2 due to bug-fix in BradleyTerry2 03-11-2010 Further reivision of mhtplot using real data from Tuomas.Kilpelainen@mrc-epid.cam.ac.uk 07-07-2010 Revise mhtplot at suggestion of Peter Ehlers [ehlers@ucalgary.ca] 30-06-2010 Replace qqplot within gcontrol2 by qqunif Version 1.0-23 24-06-2010 Refine keywords 23-06-2010 Add masize for sample size calculation in mediation analysis 08-06-2010 Add references to apoeapoc following a query from Breitling Lutz [l.breitling@Dkfz-Heidelberg.de] 27-05-2010 Rename abc as ab, pending addition of a formal abc 14-05-2010 Add hwe.cc based on codes by Chang Yu [chang.yu@vanderbilt.edu] 29-04-2010 Add ACE.R for ACE, AE, CE and E twin models using OpenMx and create h2 20-04-2010 Add mtdt2 calling BradleyTerry2 01-04-2010 Add klem with .C("kbylem") for LD statistics based on imputed SNPs to be calculated 24-03-2010 Fix problems of no specification of ylim=NULL at mhtplot 03-01-2010 Add example data to comp.score and refine makeped example Version 1.0-22 01-01-2010 Refine ccsize, fbsize and pbsize 21-11-2009 Add outfile and outfileonly arguments to read.ms.output Version 1.0-21 20-11-2009 Fix bug on read.ms.output when nsam==1 and make mhtplot to accommodate generic data as pointed by Dagmar Kapell [Dagmar.Kapell@sac.ac.uk] 19-11-2009 Add function read.ms.output after work on EJHG paper and revise link to qqfun from qqunif 10-11-2009 Add function abc based on EPIC-Norfolk data for QQR for Shengxu Li [shengxu.li@mrc-epid.cam.ac.uk] 08-11-2009 Add confidence interval option to qqunif as required by Andy Wood [arwood@pms.ac.uk] 28-08-2009 Remove references to qqline, qqplot of stats in qqfun.Rd and depreciated power.casectrl of genetics Version 1.0-20 26-08-2009 Rename kbyl as LDkl in geneecounting.Rd, add references to vignette for b2r/mvmeta Version 1.0-19 25-08-2009 Attempt to do away with warning from 2ld.c Version 1.0-18 25-08-2009 Remove braces for enumerate items in genecounting.Rd and hap.Rd 18-08-2009 Add b2r in order for meta-analysis via correlations to be conducted 17-08-2009 Add arguments alpha and beta to fbsize as needed by Tetyana Zayats [zayatst@Cardiff.ac.uk] Add mvmeta from an earlier test, pending on further work on using linear regression estimates 11-08-2009 Suggests pedigree package 23-07-2009 Fix subscript for QW in metareg as pointed by Emmanouela Repapi [er82@leicester.ac.uk] 08-06-2009 Revise mhtplot documentation example according to Meg Rose [mrose19@jhu.edu] 03-01-2009 Fix link to Citations.txt Modify gap-package.Rd and mhtplot.Rd Version 1.0-17 02-01-2009 Remove braces from Rd files according to CRAN check Version 1.0-16 02-01-2009 Refine asplot and mhtplot 01-01-2009 Modify mhtplot with real position, colors for available chromosomes, default cutoffs and gap 31-12-2008 Remove psfig.sty from gap.Rnw 14-11-2008 Change pos <- data[,2] to pos <- 1:length(data[,2]) according to Aron Chiang 07-11-2008 Add 'base' to mhtplot as pointed by Aron Chiang [Yutin.A.Chiang@uth.tmc.edu] Add detach(hapdat) to gc.em according to Jose Osorio [Jose.OSORIOYFORTEA@limagrain.com] Add comments on permutation test of r2 as for Sofiane MEZMOUK [Sofiane.MEZMOUK@biogemma.com] 20-08-2008 Revise links to LDkl in gc.em.Rd and hap.em.Rd Add HapDesign and HapFreqSE by Andrea Foulkes 23-04-2008 add mzdz.dat Version 1.0-15 10-04-2008 Rename tbyt/kbyl as LD22/LDkl and fix hap.c 07-04-2008 Add ESplot for Grace Jing Wang's query 28-03-2008 Add regional association plot (asplot) 25-03-2008 Add qqfun according to qq.plot of package car by John Fox 22-03-2008 Add gcontrol2 (experimental) 21-03-2008 Remove labels "chr" in mhtplot 20-03-2008 Swap order of x, y in qqunif 14-03-2008 Create mhtplot for Manhattan plot of genomewide p values Add example to qqunif for highlighting p values above certain threshold 10-03-2008 Revise pedtodot according to pedigrees from Jinliang Wang/Richard Mott 07-03-2008 Add Fisher's method for meta-analysis to metap 06-03-2008 Replace get() with data[""] in metap/metareg Refine metap.Rd to make it consistent with the GIANT example Document some functions in gap-internal.Rd Provide option for file of haplotype assignment 04-03-2008 Add metap, and modify metareg to accept multiple records Add PARn, snp.ES, snp.HWE, snp.PAR 03-03-2008 Add metareg 02-03-2008 Add citations.txt to inst/doc Version 1.0-14 01-03-2008 Add pbsize2 and make an internal function from pexp/fexp Add jss07.pdf to inst/doc Add mao.dat to inst/tests and therefore modify genecounting.Rd 27-02-2008 Change license to GPL (>=2) as suggested by Kurt Hornik 20-02-2008 Correct reference as suggested by Mark N Grote Change V = -1.,2.1,.1 to J = 1,32, V=-1+0.1*(J-1) in twinan90.f Version 1.0-13 01-08-2007 Refine BFDP,FPRP,qqunif Version 1.0-12 16-06-2007 Add haplo.stats to Suggest and remove associate functions 28-07-2007 Add BFDP,FPRP,qqunif Version 1.0-11 12-06-2007 Add gap-package.Rd and reformat this file with tabs 18-04-2007 Add comp.score 08-04-2007 DESCRIPTION: Suggests: Design, Hmisc Version 1.0-10 02-01-2007 Remove P1 in powerj of tscc function Rename mi.inference to micombine to avoid confusion 11-10-2006 add \method markup to plot.hap.score and print.hap.score Version 1.0-9 21-9-2006 Add Design, Hmisc to DESCRIPTION as required by R 2.4.0 Add more summary statistics to twinan90 Add mi.inference to mia Add power calculation for joint analysis of two-stage design Add recent references to gap.Rnw Version 1.0-8 04-04-2006 Add heritability estimate to twinan90 Remove unused definitions according to compiling error from Kurt Hornik Temporarily disable dependence on R/genetics due to problems with mvtnorm Version 1.0-7 01-04-2006 Remove comments about haplo.score in gap.Rnw Add twinan90 by Chris Williams Add byrow=TRUE to a number of matrix() calls Version 1.0-6 12-02-2006 Fix bug in genecounting when multiple runs of chromosome X data is used Add example to pedtodot as in R News and Bioinformatics Version 1.0-5 16-01-2006 Drop pathmix and pointer Version 1.0-4 13-12-2005 Add ccsize Version 1.0-3 24-07-2005 genecounting (gc.c): Change nhet2 from short to long (int) Change ll() in gc.c according to report by Iris Grossman on a "Crazy" data hwe.hardy: Fix bug report by Lize van der Merwe on data three=c("A/A",rep("A/B",4),rep("B/B",4),rep("A/C",14),rep("B/C",28),rep("C/C",49)) g3=genotype(three) hwe.hardy(g3) It benefits from the original author of HWE ("Guo, Sun-Wei" ) 17-04-2005 Refine 2ld.R and 2ld.c according to the C program 2LD Revisit pfm.sim.f (f95 -PIC -xlibmil -xO5 -dalign -c by Brian Ripley). Version 1.0-2 14-04-2005 Done with genecounting involving Chromosome X data. Comment on code for hrt which is useless and causes crashes. Move fine controls of genecounting and hap to gc.control/hap.control. Version 0.8-4 18-03-2005 add NAMESPACE change bt, gcontrol, mtdt add pedtodot add datasets mao, nep499, snca, cf, fa, crohn modify hwe.hardy by Gregor Gorjanc , which requires package genetics change onLoad to .onLoad Version 0.8-3 08-11-2004 Ddapt haplo.score fully for hap.score Create examples for hwe.hardy using pgc, etc. Add gcp Modify gc.em, hap.em to allow for any allele labels Change hwe to accept allele, genotype and genotype count more naturally Change digit2 and digitm from int to void because of a complaint by Brian Ripley Version 0.8-2 16-08-2004 Add keyword as required by R 2.x Change hwe.hardy.c, pgc.h and makeped.c according to gcc -Wall -pedantic Version 0.8-1 05-06-2004 Add kin.matrix to kin.morgan using algorithm similar to g2a Replace tril/triu in mtdt with standard function lower.tri/upper.tri Add resid and scale prob in genecounting Relabel gret in pgc.Rd as cdata Delete comma in pfc.R and fix problem with loop index in pfc.f Add pfc.sim Version 0.8 04-02-2004 Crashes by hwe.hardy go away, chi-squared tests to be implemented 08-02-2004 Add hwe, decided any details should go to the R code itself 17-02-2004 Add static to outfile in pgc.h and hap.c, pointed by Jan de Leeuw (deleeuw@stat.ucla.edu) 21-02-2004 Completion of the first comprehensive analysis of data on Parkinson's disease and SNCA markers from Abbas Parsian (parsian@louisville.edu) (HWE, haplotype frequency estimation, score tests, Fisher's exact test, hwde, genetics) and gap obtained comparable results with SAS combined with hwe of Jurg Ott (ott@rockefeller.edu) but dealing with missing data; this could be released as an example later on. It was decided that auxiliary functions are better added after the actual linkage analysis codes are working. Fix lr statistic in gc.em.R due to rename of lnlx to lx 26-02-2004 Reverse the order of version history in this file (starting from the most recent) Version 0.7 02-02-2004 Warnings pointed by Kurt Hornik Change %lf to %f in several places of pgc.c Remove semicolon after } of rsort1 Version 0.6 28-01-2004 Changes for Mac OS X 10.3 (Panther) according to Michael Barmada (michael.barmada@hgen.pitt.edu): . do_switch --> ndo_switch in hwe.hardy.c . malloc.h --> malloc/malloc.h in gcontrol.c and makeped.c; but it seems ok to stick to stdlib.h . add static to n_loci, etc. in hap.c, mia.c to avoid conflict 31-01-2004 Rename genecounting.R to gc.R and change lnl0 and lnl1 to l0 and l1 Add pgc function but with same problem as hwe.hardy 01-02-2004 Fix error and handle.miss functions in pgc when with.id=0 Change cat() to c() in gap.demo.R to avoid generating data files Merge muvar1 and muvar2 into muvar and add their synopsis Version 0.5 19-01-2004 To remove warnings earlier found in PC and pointed by Prof Brian Ripley Resubmission to CRAN 22-1-2004 Add haplotype diversity to genecounting Add default value to optrho in kbyl Change "for" to "with" when describing fsnps Version 0.4 14-01-2004 Create this file Change DESCRIPTION Correct author of mtdt Delete hap.out in R directory Add docoumentation of htrtable in gc.em See also pfc rather than gif in gif.Rd Add right bracket in dat1 of chow.test Change ad to y in htr.Rd and the annotation in apoeapoc.Rd Version 0.3 13-01-2004 Refine Vignette and change gap.demo.R Version 0.2 12-01-2004 Change %lf and %lg to %f according to check by Prof Kurt Hornik Version 0.1 11-01-2004 First submission to CRAN with Vignette and revised Rd 07-06-2003 Draft plan (home edition) shortly before RSS 2003