Running this process for the example.gen and the example.sample files generates the Results window shown below. Refer to the Imputed SNP (Tall Format) Input Engine process description for more information.
The Results window contains the following elements:
Output Data
This process generates the following data sets:
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Genotype Threshold Data Set: This wide data set lists the most likely genotype for each marker, provided the value exceeds the specified Genotype Probability Threshold. Alternatively, for markers for which no genotype's probability meets the specified threshold, a missing value symbol (.) is listed.
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Expected Genotype Data Set: This data set contains one column per SNP with the expected numeric genotype, where the genotype 2 represents homozygous for the minor allele, which is determined using the genotype probabilities. This data set can be used as the input to SNP-Trait Association with Format of Marker Variables set to Numeric Genotypes and only the Trend test selected to be performed.
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Genotype Probabilities Data Set: This data set contains three columns per SNP with the probability for each genotype, A/A, A/B, and B/B. This data set is in stacked format grouped by SNP
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Annotation Data Set: This data set lists on the information biological or chemical properties, such as gene identity or chromosomal location, for each of the markers/ molecular entities in the experiment. Refer to Annotation Data Sets for more information about this data set.
Note: You can view the data in a file or data set by clicking either or (when the data set is very large).
Launch Follow-up Processes
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Imputed SNP Trait Association: Click to launch the Process Description process with the output data set specified as input.
General
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Click to reopen the completed process dialog used to generate this output.
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Click to close all graphics windows and underlying data sets associated with the output.
