qtl-internal: Internal qtl functions

In byandell/qtl: Tools for analyzing QTL experiments

Description

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

Usage

calc.plod(lod, nterms, type=c("f2","bc"), penalties)
checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata,
           ind.noqtl=NULL, weights=NULL, verbose=TRUE)
clean(object, ...)
condense(object)
convert(object, ...)
convert2bcsft(cross, BC.gen = 0, F.gen = 0, estimate.map = TRUE,
              error.prob=0.0001, map.function=c("haldane","kosambi","c-f","morgan"),
              verbose=FALSE)
create.map(map, step, off.end, stepwidth=c("fixed", "variable", "max"))
find.pseudomarkerpos(cross, marker, where=c("draws", "prob"))
flipcross(cross)
genAllPartitions(n.taxa, taxa)
getsex(cross)
addmarkerstointervalmap(cross,intervalresult,verbose=FALSE)
mqm_version()
scanall(cross, scanfunction=scanone, multicore=TRUE, n.clusters=1, batchsize=10, FF=0,cofactors=NULL, ..., plot=FALSE, verbose=FALSE)
getgenonames(type=c("f2","bc","riself","risib","4way","dh","special","bcsft"),
             chrtype=c("A","X"), expandX=c("simple","standard","full"),
             sexpgm, cross.attr)
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)
## 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)
polyplot(x, type='b', legend=TRUE,legendloc=0, labels=NULL, cex =
         par("cex"), pch = 19, gpch = 21, bg = par("bg"), color = par("fg"),
         col=NULL, ylim=range(x[is.finite(x)]), xlim = NULL, main = NULL, xlab =
         NULL, ylab = NULL, add=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, ...)
replacemap(object, map)
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, ...)

Author(s)

Karl W Broman, [e-mail]

byandell/qtl documentation built on May 13, 2019, 9:28 a.m.