‹‹ Back to SVS Home

The File Menu

6.3 The File Menu

---

---

The File menu normally has the following menu items: Save As, Save As Comma-Delimited Text File, Save As DSF, Apply Gene Marker Map, Join Spreadsheet on Row Labels, Join Spreadsheets With Uneven Row Numbers, Join Spreadsheets by Sorting, Import a Legacy Tree Model and Close.

If the spreadsheet is a pedigree or family-indexed spreadsheet, the File menu will have up to the following items: Save As, Save As Comma-Delimited Text File, Save As DSF, Save as PED/MAP Files (if a marker map is applied), Save Family Data, Apply Gene Marker Map (if a markker map is not applied), Join Spreadsheet on Row Labels (if there are row labels), Join Spreadsheets With Uneven Row Numbers (if there are row labels), Join family-indexed spreadsheets, Join Spreadsheets by Sorting, Import a Legacy Tree Model and Close.

6.3.1 Save As - Exporting Data

The menu choice File->Save as opens an Export Data file dialog. The blank areas can not be filled in (they are place holders to show the selected file and format once chosen). Click the textbfBrowse button. This opens a Save As dialog window, entitled Choose a file and format to export to, that has the Save as type setting defaulting to the CSV file type. (For more information on CSV files see the topic Data Types.) The Save as type drop down menu allows the file to be saved in any number of popular data formats. When the file has been named and the file format designated, click the Save button. This returns you to the Export Data window Fig. 6.7 where you can change the Delimiter from Comma to Space or Other. The Allele delimiter can be similarly changed from Underscore(_) to Comma, Space or Other. When everything is set, click the Export button.

---

---

6.3.2 Save As Comma-Delimited Text File

Allows the saving of the spreadsheet as an ASCII, comma delimited (CSV) file. This menu choice opens a Save As dialog window. Use this dialog to navigate and name the new CSV file. This “.csv” file may then be imported by other spreadsheet programs.

6.3.3 Save As DSF File

Allows the saving of the spreadsheet as an Dataset Storage Format (DSF) file. This menu choice opens a Save As dialog window. Use this dialog to navigate and name the new DSF file. This “.dsf” file may then be imported by other users of HelixTree. See 4.3.4 for a discussion of DSF as a storage format.

6.3.4 Save As PED/MAP Files

---

---

If you have a marker mapped spreadsheet that also is a pedigree spreadsheet, you can export your data into the text PED/MAP file format used by PLINK (see section 4.3.7 for importing this file format).

Selecting this menu item will prompt you for a Save As dialog to select the destination file with a “.ped” extension. HelixTree will then save both the current spreadsheet to the selected file and the marker map to the correlated “.map” file at the location specified.

Note that the encoding for missing phenotypes is the default “-9” for the Sex and Affection Status columns and “0” for genotypes.

6.3.5 Save Family Data

If the spreadsheet is a pedigree or family-indexed spreadsheet, this option will be available. Allows the saving of the spreadsheet’s pedigree data (for a pedigree spreadsheet), in FBAT/PBAT pedigree format, or the saving of any phenotype data the spreadsheet may have, in FBAT/PBAT phenotype format.

A Save As dialog window will open. Use this dialog to navigate and name the new pedigree or phenotype file.

6.3.6 Apply Gene Marker Map

---

---

Prior to applying a Gene Marker Map from the spreadsheet view, a Gene Marker Map must be imported from the Project View window File menu. The chapter on Importing Data 4 details the importation and creation of a marker map.

The spreadsheet menu choice File->Import Gene Marker Map opens a Marker Map Chooser dialog window that highlights in white all the available files in the project folder. Click on the desired spreadsheet. If the distance column is not an integer or double, or if there are no row headers containing SNPS or markers an error message will appear.

It is possible to map some of the markers, but not map the rest. Simply do not include any information about the markers which are not to be mapped.

When the Linkage Disequilibrium or Hardy-Weinberg Equilibrium plot is displayed using map information, the markers are grouped together based on which chromosome and region they are in. The unmapped markers, if any, are grouped together before the mapped markers.

6.3.7 Join Spreadsheet on Row Labels

This feature allows two spreadsheets (data sets) with the same row labels (such as patient IDs) but different data in the columns to be merged. The columns of the second data set are appended to the right of the columns in the original data set. (The exception to that is that information from a pedigree spreadsheet will always appear first, on the left.) The merged spreadsheet creates a child Navigator Node under the first spreadsheet labeled "Joined spreadsheet".

From the spreadsheet view of the data to be added to, click the File->Join Spreadsheet on row labels menu option. A Navigator Widget Chooser dialog box opens with a list of all the available spreadsheets in the project file. Click on the spreadsheet to be joined to the opened spreadsheet. A window opens describing the success of the merger– click the OK button. The program opens the merged spreadsheet.

6.3.8 Join Spreadsheets With Uneven Row Numbers

This feature allows you to merge two spreadsheets which have common row labels while still including rows which have labels that appear in only one of the spreadsheets. Upon running the join, the columns of the second data set are appended to the right of the columns from the original data set, with the following exceptions: Columns with names that appear in both data sets will be “merged” so that any would-be missing values in the columns from the original data set will be filled in with the corresponding values from the column in the second data set if possible. The column from the second data set is then discarded.

Additionally, rows with labels that appear in only one of the spreadsheets will have missing values inserted in all columns with names that appear only in the other data set. Rows with labels that only appear specifically in the second spreadsheet will be appended to the other rows. Thus, the end result is a spreadsheet with rows matching all of the rows of the first spreadsheet, followed by the rows with labels that appear only in the second spreadsheet.

One implication of what is mentioned in the paragraph above is that you may use Join Spreadsheets With Uneven Row Numbers to append one spreadsheet to a second one.

NOTE: When using Join Spreadsheets With Uneven Row Numbers, either both spreadsheets must be pedigree spreadsheets, both spreadsheets must be phenotype spreadsheets, or both spreadsheets must neither be pedigree nor phenotype spreadsheets. The type of the resulting spreadsheet will match the one type that both input spreadsheets are guaranteed to have.

NOTE: If you use Join Spreadsheets With Uneven Row Numbers on two pedigree spreadsheets or two phenotype spreadsheets, note that matching will be done on row labels. The family and patient ID’s will be ignored in this matching process.

From the spreadsheet you wish to add to, click the File->Join Spreadsheets With Uneven Row Numbers menu option. This will open a Navigator Widget Chooser dialog box with list of all available spreadsheets in the current project. Click on the spreadsheet to be joined to the original spreadsheet, and click OK. A window will open, reporting the success of the join, as well as the number of rows which were successfully joined. Click OK to close the message, and the program will open the newly merged spreadsheet.

6.3.9 Join family-indexed spreadsheets

A family-indexed spreadsheet (pedigree or other family-indexed data) may be joined with another family-indexed spreadsheet. The family ID (which is always the first column of a family-indexed spreadsheet) and the patient ID (which is always the second column of a family-indexed spreadsheet) will both be matched between the spreadsheets. A family-indexed spreadsheet will result from the join. The columns of the second spreadsheet will appear to the right of the columns from the original spreadsheet, except that phenotypic data will generally appear before genotypic data, and there will be only one Family ID/Patient ID column pair at the beginning. The merged spreadsheet creates a child Navigator Node under the first spreadsheet labeled "Joined spreadsheet".

From the spreadsheet view of the data to be added to, click the File->Join family-indexed spreadsheets menu option. A Navigator Widget Chooser dialog box opens with a list of all the applicable spreadsheets in the project file. Click on the spreadsheet to be joined to the opened spreadsheet. A window will open, reporting the success of the join, as well as the number of rows which were successfully joined. Click the OK to close the message, and the program will open the newly merged spreadsheet.

6.3.10 Join Spreadsheets by Sorting

This feature allows joining of any two spreadsheets (data sets) regardless of row labels. The columns of the second data set are appended to the right of the columns in the original data set. The number of rows joined will be the minimum of the number of rows in the two datasets. If the rows are not in a matching order they can be reordered using the join dialog that is part of this feature.

From any spreadsheet viewer, click the File->Join Spreadsheet by Sorting menu option.

---

---

A Navigator Widget Chooser dialog box opens with a list of all the available spreadsheets in the project file listed. Click on the spreadsheet to be joined to the original spreadsheet then click the OK button. This will bring up the sorting dialog window show below. Note that the number of rows in the joined spreadsheet will be the minimum of the two selected spreadsheet. For example if one sheet has 50 rows and the second has 100 the merged spreadsheet will have 50 rows.

---

---

This window shows the original spreadsheet on the left and the selected spreadsheet on the right. The row numbers are listed by default and if there is a label column then it is also displayed. There is a drop-down list at the top of each spreadsheet that contains the first five columns of the spreadsheet in case you would like to order the rows using a different column. Selecting one of the drop down columns will add the column to the display box below the drop-down so that you can use any of the sorting tools on that column.

Using the column that you want to sort you can either sort the whole column in ascending or descending order by clicking on the title bar for that column or you can move individual rows up or down using the Move Up and Move Down buttons. These operation are done on both spreadsheet until the rows on the left and right are lined up in the order that you would like them to be joined.

The final radio button at the bottom indicates where the new dataset and spreadsheet will be put in the Project Navigator window. By default a new dataset will be created as a child of the root project node. Optionally you can have the new dataset as a child of the original spreadsheet. When everything is in order click the Begin Joining button.

When the join is complete a window opens describing the success of the merger, click the OK button. The program then opens the merged spreadsheet for your viewing.

6.3.11 Import a Legacy Tree Model

This option opens a file browser where you can select a previously created .ght file. The tree file you are importing must have the same number of columns, the same data types for each column and the same dependent variable. After importing the tree if the values displayed do not match in all three columns it indicates that the original data does not exactly match the current spreadsheet.

6.3.12 Closing the File

The File->Close menu selection closes the data file and its associated spreadsheet. A dialog window prompts for the saving of unsaved data.