The
Build QTL Genotype Probability Data Set
process
builds a
genotype
probability SAS data set. The GP (Genotype Probability) data set includes probabilities of each possible
QTL
genotype (QQ, Qq, or qq) in each location for all individuals. Locations are distributed at one
centiMorgan
(cM) intervals along each
chromosome
. The process also integrates experimental design information into its values.
The
Build QTL Genotype Probability Data Set
process
creates a data set that can be used by the
QTL IM, CIM and MIM Analysis
process for a single QTL model.
Two SAS data sets are required. The first, the
input cross file, lists information about the different genetic crosses used in the study. The
qtlbcsample_geno.sas7bdat
data set, used in the following example, is shown below. This is a wide data set with 300 individuals listed in rows and the status of individuals for two
traits
and 36 markers, spanning 3 chromosomes, listed in columns. Markers are formatted as numeric genotypes.
The second required data set is an
Annotation Data Set
that
lists map information for each of the markers.
The
qtlbcsample_anno.sas7bdat
annotation data set
, used in the following example, is shown below. This data set contains 4 columns listing the name and position (in cM) of 36 markers present on three chromosomes.
Both the
qtlbcsample_geno.sas7bdat
and the
qtlbcsample_anno.sas7bdat
data sets are located in the
Sample Data\QtlMapping
directory included with JMP Genomics.