Output Description

Partition

Running this process for the XTitrationExample sample setting generates the tabbed Results window shown below. Refer to the Partition process description for more information. 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:

Tab Viewer

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.

The following tab is generated by this process:

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Chromosome Segmentation Summary: displays the fitted partition results separately for each chromosome using a color theme to indicate value.

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Chromosome Segmentation Plots: displays detailed plots of regions on which you drill down.

Action Buttons

Action buttons provide you with an easy way to drill down into your data. The following action button is generated by this process:

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View Chromosome Segmentation Details: Specify minimum and maximum densities and click View Chromosome Segmentation Details to explore regions of interest in more detail.

Output Data

This process generates the following output data sets:

Original Rules Data Set: This data set contains the split points for each sample as well as overall cutpoints and worth statistics for each chromosome. The name of this data is set is given by the Output Prefix, or input data set name if none given, with the suffix _rules. Click Open to view the data set.

Original Summary Statistics Data Set: This data set contains the start, end, mean, standard deviation, and N statistics for each segment, as well as overall statistics for each chromosome. The name of this data is set is given by the Output Prefix, or input data set name if none given, with the suffix _sumstats. Click Open to view the data set.

Original Rules Data Set: This data set is derived from the Original Rules data set by applying cutoff filters. The name of this data is set is given by the Output Prefix, or input data set name if none given, with the suffix _filter_rules. Click Open to view the data set.

Filtered Summary Statistics Data Set: This data set is derived from the Original Summary Statistics data set by applying cutoff filters. The name of this data is set is given by the Output Prefix, or input data set name if none given, with the suffix _filter_sumstats.Click Open to view the data set.

Filtered Tall Detail Data Set: This data set expands and repeats the data from the Filtered Summary Statistics data set into a tall data set, with one row per chromosome and position and rows aligned across samples. The name of this data is set is given by the Output Prefix, or input data set name if none given, with the suffix _filter_tall. Click Open to view the data set.

Filtered Stacked Detail Data Set: This data set stacks all of the data from the Filtered Tall Detail data set so that there is only one row per sample, chromosome, and position. The name of this data is set is given by the Output Prefix, or input data set name if none given, with the suffix _filter_stacked. Click Open to view the data set.

Filtered Lite Summary Statistics Data Set: This data set summarizes the Filtered Stacked Detail data into much fewer rows for display purposes. The name of this data is set is given by the Output Prefix, or input data set name if none given, with the suffix _filter_lite. Click Open to view the data set.

Metadata Data Set: This data set contains distinct values for chromosomes, samples, and the numeric values for the current positive and negative cutoffs. The name of this data is set is given by the Output Prefix, or input data set name if none given, with the suffix _metadata. Click Open to view the data set.

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 View Data to reveal the underlying data table associated with the current tab.

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

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Click Create Report to generate a pdf- or rtf-formatted report containing the plots and charts of selected tabs.

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