This document contains a few notes describing aspects of how individual programs can be used for the exercises. Of course, for full instructions you should refer to the documentation for each program.
This is a database program which requires two files, a .dbf file which contains the actual data and a .hdc file (sometimes referred to as a header file) which describes how the data is to be displayed and what index file is to be used. An index file with extension .idc is also needed, but qdb can create this if it does not already exist. Before running qdb you might want to check that the necessary .hdc and .dbf files exist in the working directory. When you have qdb running, you should load the desired .hdc file by selecting File, Load header and then choosing the .hdc file you want. After loading the .hdc file it is a good idea to select File, Reindex in order to rebuild the indices to make sure they are up to date with the database. Data in the .dbf file can be examined and modified from the Records, Modify records menu, and data from the database can be exported in different formats using report files.
To run qdb under Windows, first check to see if it is running already by looking at the task bar. If so, just click on the button, or alternatively keep pressing Alt-tab to select it and then bring it to foreground.
If qdb is not running already, then if the executable is in a directory on the search path you can run it by clicking the Windows start button then choosing Run and entering qdb. If the executable is not on the path Windows will not be able to find it and you will have to open Windows explorer by right-clicking the Windows start button, choosing Explore, navigating to the directory containing qdb.exe and double-clicking on it (the executable file may be displayed as qdb rather than qdb.exe).
You can run qdb from the MSDOS command prompt, but if you do this then you will not be able to enter any other commands until you have exited qdb.
If you get an error message saying Cannot open HTML book.... you can ignore it - it just means that the online helpfile could not be loaded.
In order to run qdb under Unix you will need to have a graphical interface called X. Before running qdb make sure you do not have a a copy running already. Then at Unix command prompt enter:
qdb &
The ampersand means that qdb will run in "background", allowing you to enter new commands.
To quit qdb you must always use the menus and select File, Quit. You must never try to quit qdb by trying to close the frame containing it, because this can crash the X window manager. Also, you must never try to exit a menu or dialog by closing the frame, because again the window manager may crash. Instead always click on the Cancel button.
At HGMP, qdb runs in the QDB/DOLINK/PEDRAW shell from the Linkage Analysis: Linkage Utilities menu.
This is a pedigree drawing program which can display pedigree diagrams from a number of file types:
To load the data file, select File, Load ... file and then choose the one you want. Once the file has been loaded, to display a pedigree diagram select Output, Display pedigree on screen, then click OK to see a list of all subjects and choose the subject you want to see the descendants of. To get rid of the diagram either move it out of the way or minimise it, or preferably close the frame by double-clicking on the top-left corner (Windows 3.x) or clicking on the top-right corner (Windows 95).
Selecting Configure settings, Change configuration allows the user to alter how files are to be saved to disk, what titles are to be added to diagrams, and a number of other features.
To run pedraw under Windows, first check to see if it is running already by looking at the task bar. If so, just click on the button, or alternatively keep pressing Alt-tab to select it and then bring it to foreground.
If pedraw is not running already, then if the executable is in a directory on the search path you can run it by clicking the Windows start button then choosing Run and entering pedraw. If the executable is not on the path Windows will not be able to find it and you will have to open Windows explorer by right-clicking the Windows start button, choosing Explore, navigating to the directory containing pedraw.exe and double-clicking on it (the executable file may be displayed as pedraw rather than pedraw.exe).
You can run pedraw from the MSDOS command prompt, but if you do this then you will not be able to enter any other commands until you have exited pedraw.
To save diagrams to disk under Windows, select Output, Produce BMP file, then click OK to see a list of all subjects and choose an ancestor. The file can produced can subsequently be viewed with the Windows Paintbrush program.
In order to run pedraw under Unix you will need to have a graphical interface called X. Before running pedraw make sure you do not have a a copy running already. Then at Unix command prompt enter:
pedraw &
The ampersand means that pedraw will run in "background", allowing you to enter new commands.
To quit pedraw you must always use the menus and select File, Quit. You must never try to quit pedraw by trying to close the frame containing it, because this can crash the X window manager. Also, you must never try to exit a menu or dialog by closing the frame, because again the window manager may crash. Instead always click on the Cancel button.
At HGMP, pedraw runs in the QDB/DOLINK/PEDRAW shell from the Linkage Analysis: Linkage Utilities menu.
The table program is a simple utility for producing tables of lod scores from the output of mlink or linkmap, provided the output is in the form produced using lcp or dolink. It is run at the operating system prompt, and takes as its argument the name of the log file output, which conventionally has extension .res:
table filename.res
The output from table will be sent to a file called filename.tab. The program accepts a number of optional switches following the log file name, some of which are as follows:
-p produce graph files for gnuplot (.plt and .gda files)
-g produce graph file for easigraf (.grp file)
-a calculate admixture/heterogeneity lod score
-af calculate admixture lod score with alpha=f, e.g. -a0.8
-x produce graph file for ACE/gr (.xgr file)
-h produce input file for (old version of) homog (.hom file)
For example:
table filename.res -a0.75 -g
At HGMP, table runs in the FASTLINK or VITESSE shell from the Linkage Analysis: General Linkage menu.
This is a graph-drawing program available for a number of different operating systems. It reads in the data to be graphed from a graph file, and can read in instructions as to how to plot the data from a second file (or these instructions can be entered interactively). The table program can automatically produce both a suitable data file, with extension .gda, and a file containing the plotting commands, with extension .plt. When you have gnuplot running, you should load the desired plot file by selecting File, Open and then choosing the .plt file you want. The plotting commands will then cause the data to be read in from the .gda file (which must be in the same directory) and then to be displayed. At this point one can interactively change aspects of the display, for example changing the scale or switching off the key. One can then issue the Replot command and the graph will be displayed again using the new parameters.
If gnuplot is not running already, then if the executable is in a directory on the search path you can run it by clicking the Windows start button then choosing Run and entering gnuplot. If the executable is not on the path Windows will not be able to find it and you will have to open Windows explorer by right-clicking the Windows start button, choosing Explore, navigating to the directory containing gnuplot.exe and double-clicking on it (the executable file may be displayed as gnuplot rather than gnuplot.exe).
You can run gnuplot from the MSDOS command prompt, but if you do this then you will not be able to enter any other commands until you have exited gnuplot.
In order to run gnuplot under Unix you will need to have a graphical interface called X. Before running gnuplot make sure you do not have a a copy running already. Then at Unix command prompt enter:
gnuplot &
The ampersand means that gnuplot will run in "background", allowing you to enter new commands. The version of gnuplot which we have running under X is not particularly easy to use and we recommend that you use ACE/gr instead if it is available.
This is a simple graph-drawing program which will only run under MSDOS. It requires a graph file as input, and this is produced automatically by the table program, and conventionally has extension .grp. The graph file is a text file which can be examined and modified using an editor. If you are running under Windows, then before running easigraf you must make sure the window is using the full screen. If this is not the case then press Alt-Enter to toggle between a window and full screen. To run easigraf, at the MSDOS prompt enter (for example):
easigraf example.grp
The graph should be displayed. For these exercises, the only thing you are likely to want to do is to rescale the graph, which is done by entering A7 (part of the Axes menu), or to save the graph to disk, which is done by entering F1 and specifying a filename with extension .msp. This can subsequently be loaded into the Windows Paintbrush program if when you Open the file you specify that you wish to List files of type: MSP.
Quit easigraf by pressing Q. Do not toggle the window back from full screen or switch to another window until you have quit easigraf.
ACE/gr is a graphing program which only runs under X. It requires a graph file which can be produced automatically by table. To run ACE/gr, at the Unix prompt enter:
xvgr &
Then load the graph file produced by table, which has extension .xgr. To rescale the graph, click on the AS (autoscale) button to view the full graph and then click on the Z (zoom) button to view the area of the graph you are interested in.
At HGMP, ACE/gr runs in the FASTLINK or VITESSE shell from the Linkage Analysis: General Linkage menu.
The .tab file should be imported into Excel with all the lod scores lined up correctly in rows and columns. If this is not the case then close the file without saving it and start again.
In order to produce the graph, proceed as follows:
This is a postscript viewing program. It requires a postscript file such as that output by genehunter.
Alternatively, you can run the ghostview program by left-clicking the Windows start button, choosing All Programs and then navigating to the program (which may be presented as GhostGum and/or GSView). Then use the File, Open menu item to select the postscript file you wish to display.
ghostview example.ps &
or possibly:
gv example.ps &
(Replacing example.ps with the file you wish to view.)
Once the file is loaded various commands are available to adjust its appearance on screen.
All material copyright (C) Dave Curtis 1996-8
dcurtis@hgmp.mrc.ac. uk