qtl-internal               package:qtl               R Documentation

_I_n_t_e_r_n_a_l _q_t_l _f_u_n_c_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     Internal qtl functions. These are generally not to be called by
     the user.

_U_s_a_g_e:

     adjust.rf.ri(r, type=c("self","sib"), chrtype=c("A","X"), expand=TRUE)
     asnumericwithdec(x, dec=".")
     calc.genoprob.special(cross, error.prob=0.0001,
                           map.function=c("haldane","kosambi","c-f","morgan"))
     calc.pairprob(cross, step=0, off.end=0, error.prob=0.0001, 
                   map.function=c("haldane","kosambi","c-f","morgan"), map,
                   assumeCondIndep=FALSE)
     calc.plod(lod, nterms, type=c("f2","bc"), penalties)
     charround(x, digits=1)
     checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata, verbose=TRUE)
     checkformula(formula, qtl.name, covar.name)
     checkStepwiseqtlStart(qtl, formula, covar=NULL)
     clean(object)
     condense(object)
     convert(object)
     countqtlterms(formula, ignore.covar=TRUE)
     create.map(map, step, off.end, stepwidth=c("fixed", "variable"))
     deparseQTLformula(formula, reorderterms=FALSE)
     discan(cross, pheno, method=c("em","mr"),
            addcovar=NULL, intcovar=NULL, maxit=4000, tol=1e-4,
            verbose=FALSE, give.warnings=TRUE)
     dropfromqtlformula(formula, qtlnum)
     dropXcol(type=c("f2","bc"), sexpgm, cross.attr)
     effectplot.getmark(cross, mname)
     effectplot.calmeanse(pheno, mark1, mark2, geno1, geno2, ndraws, var.flag=c("pooled", "group"))
     expandf2covar(thecovar)
     find.pseudomarkerpos(cross, marker, where=c("draws", "prob"))
     fitqtlengine(pheno, qtl, covar=NULL, formula, method=c("imp", "hk"),
                  dropone=TRUE, get.ests=FALSE, run.checks=TRUE, cross.attr)
     fitstahl.estp(cross, error.prob=0.0001, m=0, tol=1e-4, maxit=4000)
     fitstahl.estp.sub(p, cross, error.prob=0.0001, m=0, thetol=1e-4, maxit=4000)
     fitstahl.este(cross, m=0, p=0, tol=1e-4, maxit=4000)
     fitstahl.este.sub(error.prob, cross, m=0, p=0, thetol=1e-4, maxit=4000)
     fitstahl.estpe(cross, m=0, tol=1e-4, maxit=4000)
     fitstahl.estpe.sub(x, cross, m=0, thetol=1e-4, maxit=4000)
     fixX4write(geno,sex,pgm,crosstype)
     fixXgeno.bc(cross)
     fixXgeno.f2(cross)
     markerforwsel(x, y, maxsize=7)
     markerforwself2(x, y, maxsize=7)
     genotab.em(dat, tol=1e-6, maxit=10000, verbose=FALSE)
     getid(cross)
     getsex(cross)
     getgenonames(type=c("f2","bc","riself","risib","4way","dh","special"),
                  chrtype=c("A","X"), expandX=c("simple","standard","full"),
                  sexpgm, cross.attr)
     grab.arg.names(...)
     imf.cf(r)
     imf.h(r)
     imf.k(r)
     imf.m(r)
     imf.stahl(r, m=0, p=0, tol=1e-12, maxit=1000)
     interpmap(oldmap, newmap)
     interpmap4scantwo(output, newmap)
     LikePheVector(pheno, n.ind, n.phe)
     locatemarker(map, pos, chr, flag)
     locate.xo(cross)
     makeSSmap(cross)
     markerloglik(cross, marker, error.prob=0.0001)
     matchchr(selection, thechr)
     ## S3 method for class 'scantwocondensed':
     max(object, lodcolumn=1,
         what=c("best", "full", "add", "int"),
         df=FALSE, na.rm=TRUE, ...)
     mf.cf(d)
     mf.h(d)
     mf.k(d)
     mf.m(d)
     mf.stahl(d, m=0, p=0)
     mybinaryrep(n)
     orderMarkers.sub(cross, chr, window=7, use.ripple=TRUE)
     parseformula(formula, qtl.dimname, covar.dimname)
     ## S3 method for class 'effectscan':
     plot(x, gap=25, ylim, mtick=c("line","triangle"),
          add.legend=TRUE, alternate.chrid=FALSE, ...)
     ## S3 method for class 'addcovarint':
     print(x, ...)
     ## S3 method for class 'addint':
     print(x, ...)
     ## S3 method for class 'compactqtl':
     print(x, ...)
     ## S3 method for class 'cross':
     print(x, ...)
     ## S3 method for class 'map':
     print(x, ...)
     ## S3 method for class 'qtl':
     print(x, ...)
     ## S3 method for class 'scanoneboot':
     print(x, ...)
     ## S3 method for class 'scantwo':
     print(x, ...)
     ## S3 method for class 'summary.addpair':
     print(x, ...)
     ## S3 method for class 'summary.compactqtl':
     print(x, ...)
     ## S3 method for class 'summary.cross':
     print(x, ...)
     ## S3 method for class 'summary.fitqtl':
     print(x, ...)
     ## S3 method for class 'summary.map':
     print(x, ...)
     ## S3 method for class 'summary.qtl':
     print(x, ...)
     ## S3 method for class 'summary.ripple':
     print(x, ...)
     ## S3 method for class 'summary.scanone':
     print(x, ...)
     ## S3 method for class 'summary.scanoneperm':
     print(x, ...)
     ## S3 method for class 'summary.scantwo':
     print(x, ...)
     ## S3 method for class 'summary.scantwo.old':
     print(x, ...)
     ## S3 method for class 'summary.scantwoperm':
     print(x, ...)
     printQTLformulanicely(formula, header, width, width2, sep=" ")
     qtlformulasymmetric(formula, qtlnum1, qtlnum2)
     read.cro.qtlcart(file)
     read.cross.csv(dir, file, na.strings=c("-","NA"),
                    genotypes=c("A","H","B","D","C"),
                    estimate.map=TRUE, rotate=FALSE, ...)
     read.cross.csvs(dir, genfile, phefile, na.strings=c("-","NA"),
                     genotypes=c("A","H","B","D","C"),
                     estimate.map=TRUE, rotate=FALSE, ...)
     read.cross.gary(dir, genfile, mnamesfile, chridfile, phefile,
                     pnamesfile, mapfile,estimate.map,na.strings)
     read.cross.karl(dir, genfile, mapfile, phefile)
     read.cross.mm(dir, rawfile, mapfile, estimate.map=TRUE)
     read.cross.qtlcart(dir, crofile, mapfile)
     read.cross.qtx(dir, file, estimate.map=TRUE)
     read.map.qtlcart(file)
     read.maps.mm(mapsfile)
     replacemap(object, map)
     revisecovar(sexpgm, covar)
     reviseqtlnuminformula(formula, oldnum, newnum)
     revisescantwodf(df)
     reviseXdata(type=c("f2","bc"), expandX=c("simple","standard","full"),
                 sexpgm, geno, prob, draws, pairprob, cross.attr)
     ripple.perm1(n)
     ripple.perm2(n)
     ripple.perm.sub(x, mat)
     roundqtlpos(x, digits = 1)
     scanone.perm(cross, pheno.col=1, model=c("normal","binary","2part","np"),
                  method=c("em","imp","hk","ehk","mr","mr-imp","mr-argmax"),
                  addcovar=NULL, intcovar=NULL, weights=NULL,
                  use=c("all.obs", "complete.obs"), upper=FALSE,
                  ties.random=FALSE, start=NULL, maxit=4000,
                  tol=1e-4, n.perm=1000, perm.Xsp=FALSE, perm.strata=NULL,
                  verbose=TRUE, batchsize=250)
     scanone.perm.engine(n.perm, cross, pheno.col, model,
                         method, addcovar, intcovar, weights, use,
                         upper, ties.random, start, maxit, tol,
                         verbose, perm.strata, batchsize=250)
     scanoneXnull(type, sexpgm)
     scantwo.perm(cross, pheno.col=1, model=c("normal","binary"),
                  method=c("em","imp","hk","mr","mr-imp","mr-argmax"),
                  addcovar=NULL, intcovar=NULL, weights=NULL,
                  use=c("all.obs", "complete.obs"),
                  incl.markers=FALSE, clean.output=FALSE,
                  maxit=4000, tol=1e-4, verbose=FALSE,
                  n.perm=1000, perm.strata, assumeCondIndep=FALSE,
                  batchsize=250)
     scantwo.perm.engine(n.perm, cross, pheno.col, model,
                         method, addcovar, intcovar, weights, use,
                         incl.markers, clean.output, maxit, tol, verbose,
                         perm.strata, assumeCondIndep=FALSE,
                         batchsize=250)
     sim.bcg(n.ind, map, m, p,
             map.function=c("haldane","kosambi","c-f","morgan"))
     sim.cc(parents, n.ril=1, type=c("sibmating", "selfing"),
            error.prob=0, missing.prob=0, m=0, p=0, step=0)
     sim.cross.4way(map, model, n.ind, error.prob, missing.prob,
                    partial.missing.prob, keep.errorind, m, p, map.function)
     sim.cross.bc(map, model, n.ind, error.prob, missing.prob,
                  keep.errorind, m, p, map.function)
     sim.cross.f2(map, model, n.ind, error.prob, missing.prob,
                  partial.missing.prob, keep.errorind, m, p, map.function)
     sim.ril(map, n.ril=1, type=c("sibmating", "selfing"), n.str=c("2","4","8"),
             m=0, p=0, random.cross=TRUE)
     subrousummaryscantwo(object, for.perm=FALSE)
     ## S3 method for class 'scantwocondensed':
     summary(object, thresholds, 
              what=c("best", "full", "add", "int"),
              perms, alphas, lodcolumn=1, pvalues=FALSE,
              df=FALSE, allpairs=TRUE, ...)
     ## S3 method for class 'addcovarint':
     summary(object, ...)
     ## S3 method for class 'addint':
     summary(object, ...)
     ## S3 method for class 'compactqtl':
     summary(object, ...)
     vbscan(cross, pheno.col=1, upper=FALSE, method="em", maxit=4000,
            tol=1e-4)
     write.cross.csv(cross, filestem="data", digits=5, rotate=FALSE,
                     split=FALSE)
     write.cross.gary(cross, digits)
     write.cross.mm(cross, filestem="data", digits=5)
     write.cross.qtlcart(cross, filestem="data")

_A_u_t_h_o_r(_s):

     Karl W Broman, kbroman@biostat.wisc.edu

