Running this process for the
GeneticMarkerExample
sample setting generates the tabbed
Results
window shown below. Output from the process is organized into tabs. Each tab contains one or more plots, data panels, data filters, and so on. that facilitate your analysis.
The
Results
window contains the following panes:
This pane provides you with a space to view individual tabs within the
Results
window. Use the tabs to access and view the output plots and associated data sets.
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Heat Map Results
: This tab displays the computed relationship matrix across samples using the JMP Hierarchical Clustering Platform. It is generated when the
Plot Relationship Matrix heat map
check box is checked.
Note
: If a
Pedigree ID
variable
was specified on the
dialog
, no tabbed output is shown.
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IBD/IBS Pairs Results
: This tab displays a
distribution
of the number of sample pairs with an Identity by Descent (
IBD
) or Identity by State (
IBS
) value above the threshold specified using the
Identity By Descent Threshold
option or
Identity By State Threshold
option, respectively.
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PCA 2D Row Scores
: This tab, which shows a
scatterplot
of
principal component
scores computed on the relationship matrix, is generated when the
Perform Principal Components Analysis
option is checked. These PCA results are useful to highlight patterns in the relationship matrix.
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PCA 3D Row Scores
: This tab, which displays a 3-D scatterplot of the first three principal components colored either by the clusters from the Hierarchical heat map or by a specified
Color Variable
, is generated when the
Include 3D plots
option is checked.
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Scree Plot (Relationship Matrix)
: This tab displays the proportion and cumulative variability in the relationship matrix explained by the number of principal components selected.
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Input Data with IBD SVD Root from Relationship Matrix
: This data set contains the original input data set appended with the calculated
SVD Root of the Relationship Matrix
. This data set is in the format necessary to run the follow-up
Q-K Mixed Model
process in order to treat the relationship matrix correctly as a
random effect
. It is created if the
Compute the root of the matrix by SVD
option is checked. If either the IBS or the Allele Sharing Similarity metric is used instead of
IBD
, the IBS or AS respectively will be shown in the output data set description.
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IBD Relationship Matrix from RelationshipMatrix
: This output data set link is generated when either a
Pedigree ID
variable is specified or the options to
Plot Relationship Matrix heat map
and
Perform Principal Components Analysis
are both unchecked and a 0 value is specified for either the
Identity By Descent Threshold
or the
Identity By State Threshold
.
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For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
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Q-K Mixed Model
: Click
to launch the
Q-K Mixed Model
process with the input data with appended SVD root matrix (listed in the
Output Data
Pane above) and the
annotation data set
(optional) preloaded as input. Note: This follow-up process is available only if the
Compute the root of the matrix by SVD
option is checked.
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Multidimensional Scaling
: Click
to launch the
Multidimensional Scaling
process with the relationship matrix output data set preloaded as input. This process enables you to visualize the patterns in the relationship matrix using a dimension reduction technique.
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K Matrix Compression
: Click
to launch the
K Matrix Compression
process with the relationship matrix output data set and the original input data set preloaded as input. This process compresses the size of the matrix before using it as the random effect in a
Q-K Mixed Model
analysis.
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Click
to reveal the underlying data table associated with the current tab.
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Click
to reopen the completed process dialog used to generate this output.
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Click
to generate a
pdf
- or
rtf
-formatted report containing the plots and charts of selected tabs.
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Click
to close all graphics windows and underlying data sets associated with the output.
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