marker.levels {bqtl} | R Documentation |
The coding scheme used to define marker.levels is set up by these functions. BQTL has defaults that these functions can help the user to redefine.
bc1.levels( AA="AA", Aa="Aa", miss.val="--") ri.levels( AA="AA", aa="aa", miss.val="--") f2.levels( AA="AA", Aa="Aa", aa="aa", not.aa="A-", not.AA="a-", miss.val="--")
AA |
Always used: the code for the homozygous state from one parent line |
Aa |
F2 and BC1 setups: the code for the heterozygous state |
aa |
F2 and RI setups: the code for the homozygous state for the other parent line |
not.aa |
F2 only: the code for a dominant marker that rules out aa |
not.AA |
F2 only: the code for a dominant marker that rules out AA |
miss.val |
The character string for a missing (unknown) allele
state. NA s are automatically detected, so this is only needed
if string values are used to denote missing values. |
It is essential that the codes intended by the user be clearly understood by BQTL. It is hoped that thees functions provide a bridge between the internals of BQTL and the user's view of the marker codes. Numeric values can be used, but they will be coerced to character values.
A vector with 6 elements corresponding to the values of
AA, \code{Aa}, \code{aa}, \code{not.aa}, \code{not.AA}, and
\code{miss.val}. For RI and BC1 setups, those that do not apply will
be unnamed and set to \code{"nil"}
Charles C. Berry cberry@ucsd.edu
### show the defaults: f2.levels() bc1.levels() ri.levels() ### suppose that 1,2,3 are codes used in F2: f2.levels(1,2,3) ### show what would happen changing "Aa" to "H" f2.levels(Aa="H") bc1.levels(Aa="H")