marker.levels: 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="--")
make.analysis.obj(data, map.frame, marker.frame,
marker.levels=f2.levels(),method="F2")

Arguments

Always used: the code for the homozygous state from one parent line

F2 and BC1 setups: the code for the heterozygous state

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. NAs are automatically detected, so this is only needed if string values are used to denote missing values.

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. 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"

[object Object] make.analysis.obj

### 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") manip