qtl-internal {qtl} | R Documentation |
Internal qtl functions.
addqtl(cross, qtl, add.chr, add.pos, add.name, map) adjust.rf.ri(r, type=c("self","sib"), 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) convert.cross(cross) create.map(map, step, off.end) discan(cross, pheno.col=1, method=c("em","mr"), x.treatment, maxit=4000, tol=1e-4) dropqtl(qtl, drop) fixXdata(type=c("f2ss","f2","bc"), x.treatment=c("simple","full"), sexpgm, geno, prob, draws, pairprob) getsex(cross) getgenonames(type=c("f2","bc","f2ss","riself","risib","4way"), chrtype=c("A","X"), x.treatment=c("simple","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) pull.chr(cross, chr) read.cro.qtlcart(file) read.cross.csv(dir, file, sep=",", 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) 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) 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, x.treatment=c("simple","full"), upper=FALSE, ties.random=FALSE, start=NULL, maxit=4000, tol=1e-4, n.perm=1000, trace=TRUE) scantwo.perm(cross, pheno.col=1, method=c("em","imp","hk","mr","mr-imp","mr-argmax"), addcovar=NULL, intcovar=NULL, weights=NULL, x.treatment=c("simple","full"), 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) print.summary.fitqtl(x, ...) print.summary.cross(x, ...) print.summary.ripple(x, ...) print.summary.scanone(x, ...) print.summary.scantwo(x, ...) replaceqtl(cross, qtl, replace, by.chr, by.pos, by.name, map) vbscan(cross, pheno.col=1, x.treatment, upper=FALSE, method="em", maxit=4000, tol=1e-4) write.cross.csv(cross, filestem="data", chr, digits=5) write.cross.gary(cross, chr, digits) write.cross.mm(cross, filestem="data", chr, digits=5) write.cross.qtlcart(cross, filestem="data", chr)
These are generally not to be called by the user.
Karl W Broman, kbroman@jhsph.edu