4. Haplotype Frequency Tables

Once you define a given haplotype block you can then investigate haplotype and diplotype frequency estimations for the entire population – broken down by cases and control if applicable – and each individual sample in the dataset.

A. Generating Frequency Tables

• From the –log10 P + LD plot, select the Haplotype Block Set item in the Graph Control Interface and click the Haplotype Tables button in the Item tab.
• Keep the default values, except make sure that Per sample EM, Per sample diplotype, and Overall haplotype frequencies are selected and click Run.

Figure 5a. List of SNPs in Node Change Log.

This will create three tables, one for each selected in the previous window.

The Haplotype Table contains overall haplotype frequencies for the entire sample set. Notice that only the first marker is listed in the row label column along with the various alleles represented in the haplotype.

• To see all the SNPs in the haplotype block go to the Project Navigator and select the Block #2 - Haplotype Table node. All SNPs are listed in the Node Change Log in addition to other summary statistics (Figure 5a).

The Block #2 - EM Frequencies Table displays the various genotypes for each sample and their respective frequency estimations for each haplotype calculated with the EM algorithm.

The Block #2 - Diplotype Table displays each sample’s haplotype pair, combined as diplotypes, and each diplotype’s respective frequency estimations.