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="--")

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

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 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.

Author(s)

Charles C. Berry cberry@ucsd.edu

See Also

make.analysis.obj

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")