marker.levels {bqtl} | R Documentation |
Define marker level codes
Description
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.
Usage
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="--")
Arguments
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 |
not.AA |
F2 only: the code for a dominant marker that rules out |
miss.val |
The character string for a missing (unknown) allele
state. |
Details
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.
Value
A vector with 6 elements corresponding to the values of
AA
, Aa
, aa
, not.aa
, not.AA
, and
miss.val
. For RI and BC1 setups, those that do not apply will
be unnamed and set to "nil"
Author(s)
Charles C. Berry cberry@ucsd.edu
See Also
Examples
### 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")