Process Description

Build QTL Genotype Probability Data Set

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.

What do I need?

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.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

The output of this process includes one data sets listing the probabilities of observing specific QTL genotypes at each one cM interval along the chromosome(s). Refer to the Build QTL Genotype Probability Data Set output documentation for more information.