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:

     addqtl(cross, qtl, add.chr, add.pos, add.name, map)
     adjust.rf.ri(r, type=c("self","sib"), chrtype=c("A","X"), expand=TRUE)
     calc.pairprob(cross, step=0, off.end=0, error.prob=0.0001, 
                   map.function=c("haldane","kosambi","c-f","morgan"), map)
     checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata, verbose=TRUE)
     clean(object)
     condense(object)
     convert(object)
     create.map(map, step, off.end, stepwidth=c("fixed", "variable"))
     discan(cross, pheno, method=c("em","mr"),
            addcovar=NULL, intcovar=NULL, maxit=4000, tol=1e-4,
            verbose=FALSE)
     dropqtl(qtl, drop)
     dropXcol(type=c("f2","bc"), sexpgm, 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)
     getid(cross)
     getsex(cross)
     getgenonames(type=c("f2","bc","riself","risib","4way"),
                  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)
     locatemarker(map, pos, chr, flag)
     locate.xo(cross)
     makeSSmap(cross)
     ## 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)
     parseformula(formula, qtl.dimname, covar.dimname)
     ## S3 method for class 'cross':
     print(x, ...)
     ## S3 method for class 'map':
     print(x, ...)
     ## S3 method for class 'scantwo':
     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.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, ...)
     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)
     replaceqtl(cross, qtl, replace, by.chr, by.pos, by.name, map)
     revisecovar(sexpgm, covar)
     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)
     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)
     scanone.perm.engine(n.perm, cross, pheno.col, model,
                         method, addcovar, intcovar, weights, use,
                         upper, ties.random, start, maxit, tol,
                         verbose, perm.strata)
     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)
     scantwo.perm.engine(n.perm, cross, pheno.col, model,
                         method, addcovar, intcovar, weights, use,
                         incl.markers, clean.output, maxit, tol, verbose,
                         perm.strata)
     sim.bcg(n.ind, map, m, p,
             map.function=c("haldane","kosambi","c-f","morgan"))
     sim.cc(parents, n.ril=1, error.prob=0, missing.prob=0, m=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, n.str=c("2","4","8"), m=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, ...)
     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@jhsph.edu

