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.

_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, 
                   map.function=c("haldane","kosambi","c-f","morgan"))
     checkcovar(cross, pheno.col, addcovar, intcovar)
     checkrf(cross, threshold)
     convert.cross(cross)
     create.map(map, step, off.end)
     discan(cross, pheno.col=1, method=c("em","mr"),
            maxit=4000, tol=1e-4)
     dropqtl(qtl, drop)
     fixX4write(geno,sex,pgm,crosstype)
     fixXgeno.bc(cross)
     fixXgeno.f2(cross)
     getsex(cross)
     getgenonames(type=c("f2","bc","f2ss","riself","risib","4way"),
                  chrtype=c("A","X"), expandX=c("simple","standard","full"),
                  sexpgm)
     imf.cf(r)
     imf.h(r)
     imf.k(r)
     imf.m(r)
     locatemarker(map, pos, chr, flag)
     makeSSmap(cross)
     mf.cf(d)
     mf.h(d)
     mf.k(d)
     mf.m(d)
     parseformula(formula, qtl.dimname, covar.dimname)
     print.summary.cross(x, ...)
     print.summary.fitqtl(x, ...)
     print.summary.map(x, ...)
     print.summary.ripple(x, ...)
     print.summary.scanone(x, ...)
     print.summary.scantwo(x, ...)
     read.cro.qtlcart(file)
     read.cross.csv(dir, file, na.strings=c("-","NA"),
                    genotypes=c("A","H","B","D","C"),
                    estimate.map=TRUE, ...)
     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)
     reviseXdata(type=c("f2ss","f2","bc"), expandX=c("simple","standard","full"),
                 sexpgm, geno, prob, draws, pairprob)
     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","mr","mr-imp","mr-argmax"),
                  addcovar=NULL, intcovar=NULL, weights=NULL,
                  upper=FALSE, ties.random=FALSE, start=NULL, maxit=4000,
                  tol=1e-4, n.perm=1000, trace=TRUE)
     scanoneXnull(type, sexpgm)
     scantwo.perm(cross, pheno.col=1,
                  method=c("em","imp","hk","mr","mr-imp","mr-argmax"),
                  addcovar=NULL, intcovar=NULL, weights=NULL,
                  incl.markers=FALSE, maxit=4000, tol=1e-4, trace=FALSE,
                  n.perm=1000)
     sim.cross.4way(map, model, n.ind, error.prob, missing.prob,
                    partial.missing.prob, keep.errorind, map.function)
     sim.cross.bc(map, model, n.ind, error.prob, missing.prob,
                  keep.errorind, map.function)
     sim.cross.f2(map, model, n.ind, error.prob, missing.prob,
                  partial.missing.prob, keep.errorind, map.function)
     subset.scantwo(x, chr, ...)
     vbscan(cross, pheno.col=1, upper=FALSE, method="em", maxit=4000,
            tol=1e-4)
     write.cross.csv(cross, filestem="data", digits=5)
     write.cross.gary(cross, digits)
     write.cross.mm(cross, filestem="data", digits=5)
     write.cross.qtlcart(cross, filestem="data")

_D_e_t_a_i_l_s:

     These are generally not to be called by the user.

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

     Karl W Broman, kbroman@jhsph.edu

