Process Description

Missing Genotype by Trait Summary

The Missing Genotype by Trait Summary process tests whether there are significant differences in missing genotype proportions between cases and controls (or any two groups as defined by a binary trait variable) for each individual marker. The p-values from these tests are displayed in a plot along the marker map as are the number of missing genotypes in each trait group. Distributions for the number of missing genotypes across all markers are also displayed for each trait group.

The Missing Genotype by Trait Summary process tests whether missing genotypes at a particular marker are related to a trait. It should therefore be run before running any association testing.

What do I need?

Two data sets are needed to run the Missing Genotype by Trait Summary process. The first, the Input Data Set, contains all of the marker data. The samplegmdata_missgeno.sas7bdat data set used in the following example was generated from the samplegmdata.sas7bdat data set described in Data Sets Used in JMP Genomics Processes. This data set was computer generated and consists of 1000 rows of individuals with 130 columns corresponding to data on these individuals. Data for 60 markers is presented in the two-column allelic format in columns ma1-ma120. Modifications, found in the samplegmdata_missgeno.sas7bdat data set, include the conversion of the marker data from the two-column allelic format to the one column genotypic format (60 columns, g1-g60), in which the alleles are delimited by a / and selective elimination of data at different markers in different individuals. 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.

Examine the input data set.

Note that marker data is in the genotypic format. Missing data are indicated by blank cells.

The 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 annotation data set used in this example, the samplemap.sas7bdat data set, was computer generated and identifies markers, location and gene identities. 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 markers to be matched appropriately.

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 Missing Genotype by Trait Summary output documentation for detailed descriptions and guides to interpreting your results.