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14.3 The File Menu

Figure 14.9:

LD Plot File Menu

In addition to saving bitmaps and printing, the Linkage Disequilibrium plot has several outputs (either spreadsheet or comma-separated-value (CSV) file) available under the File menu (Fig.14.9). The first is a summary of the entire plot. The next four outputs are certain statistical values computed for any individual point. Each such output will only relate to whichever point has values on display in the lower-left corner of the plot window. The final menu option outputs SNP tags for the markers shown on the bottom axis, which are first found using the Carlson method. The file menu options are as follows:

14.3.1 Create Bitmap

Figure 14.10:

The menu choices File->Create Bitmap opens a Save As file dialog window for navigating and saving the BMP file.

Figure 14.11:

Bitmap of the LD plot with all HelixTree controls, such as buttons, pull downs and menus, removed.

14.3.2 Print Image

Figure 14.12:

The menu choices File->Print Image opens a Print dialog window.

14.3.3 Summarize Data for All Points to CSV File

Figure 14.13:

LD data summarized in a spreadsheet

Use the menus File->Summarize Data for All Points to save and export the summary data as a comma-separated-value text (CSV) file. The CSV file is organized as one row for every point with just a few columns, so it may be handled easier by spreadsheet software. Figure 14.13 shows the data loaded into a spreadsheet.

Note that for the initial (un-zoomed) display, only the data above the diagonal is exported, because this plot is symmetric around the diagonal. For a zoomed display, all points which are showing will be output, even if some may redundantly occur on both sides of the diagonal.

The fields for this output are as follows:

Field	Value
Marker1	The X-coordinate marker
Marker2	The Y-coordinate marker
Distance	The distance between the two markers
Chi Squared	Statistic on the correlation between marker1 and marker2
p Value (Chi Sq.)	The corresponding p-value for Chi square
Neg Log p (Chi Sq.)	The negative logarithm base 10 of p-value
LD Correlation R	The correlation measure between marker1 and marker2
D Prime	This is an alternative measure of linkage disequilibrium

14.3.4 Output Genotypes for Current Point to CSV File

Figure 14.14:

LD Genotypes output to spreadsheet

Use the menus File->Output Genotypes for Current Point to save and export the genotype data as a comma-separated-value text (CSV) file. This file contains the counts of marker/genotypes for a selected coordinate. Figure 14.14 shows the data loaded into a spreadsheet.

The fields for this output are as follows:

Field	Value
Marker	The name of the X-axis marker or of the Y-axis marker for this point will appear here.
Genotype	The genotype in the above-named marker, in a_b format
Count	The count of this genotype at this marker

14.3.5 Output Genotype Combinations for Current Point

Figure 14.15:

LD Combined Genotypes output to spreadsheet

Use the menus File->Output Genotype Combinations for Current Point to save this file. Figure 14.15 shows the data loaded into a spreadsheet.

The fields for this output are as follows:

Field	Value
Marker 1	The X-axis marker
Marker 2	The Y-axis marker
Genotype 1	A genotype at marker 1
Genotype 2	A genotype at marker 2
Count	The number of times Genotype 1 and Genotype 2 occur together in the same person

14.3.6 Output Allele Counts for Current Point

Figure 14.16:

Output of allele counts for a selected point

Use the menus File->Output Allele Counts for Current Point to save this file. This saves the allele counts for a selected point in the plotted matrix. Figure 14.16 shows the data loaded into a spreadsheet.

The fields for this output are as follows:

Field	Value
Marker	This shows either the x-axis marker name or the y-axis marker name
Allele	An allele for the named marker
Count	The number of occurrences of this allele in the named marker
Freq	The probability for this allele at this marker

14.3.7 Output Allele Combinations for Current Point

Figure 14.17:

Output of allele combinations for a current point

Use the menus File->Output Allele Combinations for Current Point to save this file. Figure 14.17 shows the data loaded into a spreadsheet.

The purpose of this file is to answer the question: “For every allele from the x-axis marker and every allele from the y-axis marker, how does the actual probability of finding this combination compare with the expected probability of finding it?”

The fields for this output are as follows:

Field	Value
Marker 1	The x-axis marker
Marker 2	The y-axis marker
Allele 1	An allele for the x-axis marker
Allele 2	An allele for the y-axis marker
Combination Count	The number of occurrences of this allele combination at this point
Nij Over n	The probability of this combination at this point
Freq 1	The probability for this x-axis allele
Freq 2	The probability for this y-axis allele
Delta ij	The difference between the actual and expected combination probabilities
Chi Squared ij	Chi squared resulting from this combination
D Prime ij	The D Prime number resulting from this combination
Chi Square Contrbn	The contribution from this combination to the point’s entire Chi squared value
D Prime Contrbn	The contribution from this combination to the point’s entire D Prime value
(DAA)	Hardy-Weinberg coefficient D_AA for the first allele of marker 1 (biallelic HW-corrected case only).
(DBB)	Hardy-Weinberg coefficient D_BB for the first allele of marker 2 (biallelic HW-corrected case only).

14.3.8 View Carlson-Method SNP Tags

This option finds and shows the result of SNP-tagging on the markers currently showing on the X-axis using the Carlson method.

This option may also be requested by clicking the “C” icon on the toolbar.

Figure 14.18:

LD Plot Carlson SNP-Tagging Option

The Carlson (see [Carlson 2004]) method, which is based completely on the R² LD statistic, determines groupings of markers which are in tight correlation with an individual marker or markers (tagging markers) within the grouping. Markers whose minor-allele frequency (MAF) is not sufficiently high are not considered for designation as tagging markers.

NOTE: This method is designed to work best where the markers are individual SNPs without missing data.

When this option is selected, the following dialogue appears. In it, you select the thresholds that you want to use for the minor-allele frequency (MAF) and for the R² statistic. In addition, you can limit the separation of pairs of markers being considered for groupings; that is, you can use this method over a narrow window of markers that are more likely to yield pairs of markers which are in LD. To do this, check the “Check for Marker Correlation Only Within Window” checkbox and enter the window size.

Figure 14.19:

Carlson SNP-Tagging Options

After some computation, a spreadsheet will appear.

The fields for this output are as follows:

Field	Value
Name	The name of the marker
Minor Allele Freq	The minor-allele frequency of the marker
Minimum LD R^2	The minimum R² LD statistic existing between this marker and any other marker in its group
Tag?	Whether or not this marker is usable as a tag for this group
Tag Group	The number of the group into which this marker has been placed, or zero if the marker is not in a group

Figure 14.20:

Carlson SNP Tags

In order to better view the groupings, sort the spreadsheet by column 4, the grouping number.

Figure 14.21:

Grouped Carlson SNP Tags

“Group 0”, if present, represents those markers with insufficient minor-allele frequency to be grouped or to be used as tags. Group 1 will be the largest group, since the Carlson method finds the largest possible groupings first, then out of the remaining markers, finds the next-largest possible grouping, etc. The final groups may consist of singleton markers, that is, those which do not have sufficient R² LD with any other marker to be grouped.

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