ricalc-internal: Internal ricalc functions

In kbroman/ricalc: Calculations for Recombinant Inbred Lines

Internal ricalc functions

Description

Internal ricalc functions.

Usage

adjust.order(string, chrtype=c("A","X"))
alternates(pat, n.strains=c("2","4"), chrtype=c("A","X"))
create.parent(L, allele=1)
cross(mom, dad, m=10, obligate.chiasma=FALSE, xchr=FALSE, male=FALSE, sexsp=1)
exchangeg(string,alle=c("A","B"))
get.meiosis.tm(r, coinc=1, n.strains=c("2","4"), chrtype=c("A","X"),
         n.loci=c("2","3"))
get.meiosis.tm.symbolic(n.strains=c("2","4"), chrtype=c("A","X"),
         n.loci=c("2","3"))
gtypes(n.strains=c("2","4"), type=c("sibpair","ind","hap"),
         chrtype=c("A","X"), n.loci=c("2","3"), use.symmetry=TRUE,
         verbose=TRUE)
lengthHet(chr)
lennum.het(chr)
meiosis(parent, m=10, obligate.chiasma=FALSE)
meiosis.sub(L, m=10, obligate.chiasma=FALSE)
modifyL(ind, factor)
my.kronecker(a, b, sep="|")
my.kronecker.symbolic(a, b, sep="|")
nubreak(ind)
read.full.tm.symbolic(file, n.strains=c("2","4"), type=c("selfing","sibmating"),
         chrtype=c("A","X"), n.loci=c("2","3"))
read.meiosis.tm.symbolic(file, n.strains=c("2","4"), chrtype=c("A","X"),
         n.loci=c("2","3"))
reverseg(string)
where.het(ind)
write.full.tm.symbolic(file, n.strains=c("2","4"), type=c("selfing","sibmating"),
         chrtype=c("A","X"), n.loci=c("2","3"))
write.meiosis.tm.symbolic(file, n.strains=c("2","4"), chrtype=c("A","X"),
         n.loci=c("2","3"))
write.sparse(file=NULL,n.strains=c("2","4"),type=c("selfing","sibmating"),
         chrtype=c("A","X"),n.loci=c("2","3"), where=c("math","perl"))

Details

These are generally not to be called by the user.

Author(s)

Karl W Broman, [e-mail]

kbroman/ricalc documentation built on May 17, 2023, 11:54 p.m.