Output Description

Kinship Matrix

Running this process for the GeneticMarkerExample sample setting generates one output data set accessed from a Results window shown below. Refer to the Kinship Matrix process description for more information about this process.

The Results window contains the following panes:

Output Data

This process generates the following output data set:

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Output Kinship Data Set: The output data set represents a modification of the input data set. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _kmx. Click Open to view the data set (shown below).

The value of 0, listed in the father and mother columns in the input data set, identifies the parents in the different pedigrees. The parents of these individuals are not included in the data set, and thus these values are replaced in the output data set by the missing (.) symbol.

The results of the kinship matrix process are listed in new columns, listing the size of each of the pedigrees, the type of matrix coefficients calculated and the matrix entries themselves, in this case the Cholesky root of each pedigree's covariance matrix (COL1-COL7).

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

Launch Follow-up Processes

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Q-K Mixed Model: Click Q-K Mixed Model to launch the Q-K Mixed Model process with the output Kinship data preloaded as input. Note: This follow-up process is not available when the Inbreeding Coefficient radio button is selected as the Kinship Matrix Diagonal.

General

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Click Reopen Dialog to reopen the completed process dialog used to generate this output.

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Click Close All to close all graphics windows and underlying data sets associated with the output.