Output Description

Recode Genotypes

Running this process for the GeneticMarkerExample sample setting generates two output data sets accessed from a Results window shown below. Refer to the Recode Genotypes process description for more information about this process.

The Results window contains the following panes:

Output Data

This process generates the following output data sets:

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Output Genotype Data Set: The output data set containing the genotype data from the input data set recoded as specified in the process dialog. In this example, the input data set was converted from a two-column to a one-column format. Furthermore, markers were relabeled at each locus using the names supplied by the annotation data set. Compare the genotypes at marker 1 for the first 10 individuals (shown below).

The panel on the left, which comes from the input data set, shows the genotypes for the first ten individuals at marker 1, in the two-column allelic format. Two alleles are present at this locus, with allele "1" being the most common. The panel on the right, which comes from the output data set, shows the same data; the genotypes have been converted to the one-column, genotypic format, and recoded for analysis. Individuals homozygous for allele 2, the least common or minor allele, are represented in the output with a "2", whereas the heterozygotes are represented with a "1". Examination of additional individuals and different marker loci shows that homozygotes for the most common allele are represented in the output with a "0".

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Annotation Data Set: This data set contains all of the annotation data from the input annotation data set along with additional columns containing the names of the original allele columns that were concatenated to make a genotype column, and the new _MajorAllele_ and _MinorAllele_ columns, indicating which alleles are the major and minor alleles, respectively, for that marker.

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

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.