Process Description

LD Block Creation

The LD Block Creation process uses the LD measure Dprime (calculated by PROC ALLELE) between pairs of SNPs and creates blocks of consecutive SNPs based on those in strong LD according to thresholds set. An interactive LD plot can be viewed for each chromosome or other group variable.

The blocking algorithm is described by Gabriel et al. (2002) and Wall and Pritchard (2003). The approximate variance of Dprime for forming confidence intervals is given by Zapata et al. (1997).

What do I need?

One Input Data Set, containing all of the marker data, is required for this process. The sample data set used in the following example, the morocco_snps1exp.sas7bdat data set, represents the data from a study of gene expression variation and SNP associations in southern Morocco (Idaghdour, Czika, et al., 2010).

Note: The data was modified slightly to preserve anonymity of subjects.

It lists genotype data at 4746 SNPs in 193 individuals. Marker data is presented in the one-column format. This data set is partially shown below. Note that this is a wide data set; markers are listed in columns, whereas individuals are listed in rows.

A second, optional, data set is the Annotation Data Set. This data set contains information, such as gene identity or chromosomal location, for each of the markers. The morocco_anno.sas7bdat annotation data set is used in this example. A portion of this data set is illustrated below. This data set is a tall data set; each row corresponds to a different marker.

Note: The top-to-bottom order of the rows in the annotation data set matches the left-to-right order of the columns in the input data set. This correspondence is required for this process.

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 generated by this process is summarized in a Tabbed report. Refer to the LD Block Creation output documentation for detailed descriptions and guides to interpreting your results.