QTX
Revision History
version b20 -- 4/19/04
new features
- The numerical results of a bootstrap analysis are now presented in a
separate window.
minor bug fixes
- Fixed a problem with the Interval Mapping window which caused to not to
save the entire window.
- Fixed the format of data exported for Pseudomarker.
- Fixed a bug with caused a crash during some complex sequences of editing
operations on a user-defined map distance.
- Fixed bug #197: If you drag a chromosome out of the dataset window in
order to create a new dataset window, and then try to drag another chromosome
into the new window or drag the original chromosome out of the new window,
nothing happens.
- Fixed the problem that when chromosomes were cut or cleared from a dataset,
loci they contained were not removed from backgrounds of traits.
- Fixed a bug which caused the Interaction report to crash if there were
in the dataset only two chromosomes each with only one locus.
- Fixed bug: When I try to do a QTL regression in our newer version Map
Manager OS X, for Body Weight for either Female or Male Progeny orders.
It gives me the message "32767 to 0 informative progeny for Progeny
order " female or male.
- Fixed: When you try to "open" a file which is not a QTX file
nothing happens
version b19 -- 10/01/03
new features
- A single Mac version that will run on OS 9, OS X, and OS X Classic mode.
minor bug fixes
- Fixed crash for map window when chromosome contains only one locus.
- Fixed problem with changing trait value to unknown in dataset with more
than 500 progeny.
- Fixed problem with values of new trait sometimes being assigned 0.0 instead
of unknown.
- Fixed cosmetic problem with resizing windows.
version b18 -- 7/25/03
new features
- QTX version for Mac OS X. This is distinct from the b18 version for OS
9; the OS X version will not run on OS 9 and vice versa.
major bug fixes
- Fixed a bug which, in the OS X version, caused a crash if progeny were
sorted for a chromosome containing no visible loci. Added a message to explain
the situation
- Fixed a crash caused by editing a set while a chromosome window was open
with some order other than internal selected.
minor bug fixes
- After created a new trait, it was possible to close windows in such a
way that the "Window / Close" function would be available with
no windows open and would cause a crash if chosen.
- Fixed the"Hide by / Unlabelled" command so that it will hide
loci even if they have been created without the "unlabelled" attribute
explicitly set.
- Several changes made related to the display of datasets with more than
500 progeny.
version b17 -- 10/16/02
new features
- Modified three windows--the Genotype window, the trait edit dialog, and
the trait window--to accommodate datasets with more than 600 progeny. In
particular, modified the windows to display up to 500 progeny and added
"Next 500" and "Previous 500" buttons for datasets with
more than 500 progeny.
- Added a "User Distance" item to the Chr menu. This command changes
all inter-locus map distances to user-defined distances, for either a selected
chromosome or the whole dataset. This, in effect, freezes the map distances
at the current values.
- When an RI dataset is expanded to an RIX dataset, QTX first freezes all
map distances at the value defined by the recombinant inbred data, using
the function described above. This step is necessary to avoid having map
distances distorted by the calculated genotypes of the hybrids generated.
major bug fixes
- Fixed a problem with the regression calculations for interval mapping
for an F2 with the free regression model and no loci or traits in the background.This
bug causes little effect if markers are closely spaced (<20 cM), but
may cause a spurious LRS peak to appear midway between widely spaced markers.
It may also cause a permutation test to produce unreasonably high significance
thresholds. This problem was introduced with version b14.
minor bug fixes
- Activation of QT > Interaction menu item when a chromosome window is
frontmost.
- Activation of Option menu items when a Find dialog is frontmost.
- Enabled QT > Residual when a trait window is frontmost
- Crash when using Hide Redundant Loci in a dataset with an empty chromosome.
- Display of trait value in Note window under some circumstances.
- Problem with the name of a trait created by the Residual command.
- Activate Save command for a dataset after adding to the background of
a trait.
- Problem with updating the permutation and bootstrap sampling progress
windows.
version b16 -- 9/4/02
new features
- Boostrap analysis to estimate confidence regions for QTLs. This analysis
is activated by a checkbox option of interval mapping. QTX creates multiple
modified datasets by random resampling with replacement. For each modified
dataset, it repeats the interval mapping and records the location of the
LRS maximum. The locations of these maxima are presented as a histogram
that expresses how frequently the maximum appears in each location.
- File > Export > Map now exports either interval or cumulative map
data depending on the setting of the Chromosome Map View preference. The
map import function still imports only interval distances.
- A "Progeny Order" submenu has been added to the Chr menu. This
duplicates the function of the progeny order popup menus in the chromosome
windows, but it allows progeny orders to be applied to many chromosomes
simultaneously. If the dataset window is frontmost, the chosen progeny order
will be applied to all selected chromosomes.
removed features
- "Remove Duplicates" menu item removed from Progeny menu because
it no longer has a relevant function.
bug fixes
- Speed of the permutation test of Mac version greatly improved.
- When a single trait is selected for interval mapping, QTX uses the progeny
order of the trait for mapping. When multiple traits are selected for interval
mapping, QTX uses the progeny order of the chromosome.
- The trait editing dialog caused a crash when used with more than about
600 progeny. That limit has been raised to about 1800.
version b15 -- 6/04/02
bug fixes
- Fixes marker regression routine that ignored trait variances when they
were provided.
- Fixes "invalid rectangle" error messages occur during interaction permutation
test.
- Fixes interaction mapping that failed to generate report or crashed during
display of report.
version b14 -- 05/10/02
language changes
- The term "genotype" is now used throughout for marker typings,
even dominant marker typings that are, strictly speaking, phenotypes. The
term "phenotype" is now used only for quantitative trait values.
- The "QT Links" menu item is now labelled "Marker regression".
new features
- A new search function is available that searches for interacting QTLs.
This tests all pairwise combinations of marker loci in a range of chromosomes
for significant association with the trait, using a model that includes
interaction effects. If this association is significant, the function reports
separate likelihood ratio statistics for the interaction(s) and for each
main effect.
- A new function called Quick Test estimates the threshold for significance
of QTL by a method described in (Piepho H-P (2001). A quick method for computing
approximate thresholds for quantitative trait loci detection. Genetics 157(1):
425-432).
- A new function allows you to create a new quantitative trait that represents
the residual of a trait after subtracting the trait values predicted by
the marker loci and cofactors in the background of that trait. This residual
trait can be used in a permutation test to establish the significance standards
for detection of the next QTL in a multi-QTL model.
- The marker regression report now includes a simple estimate of the confidence
interval for putative QTLs detected by marker regression.Since the confidence
interval is often larger than expected, this estimate is a useful caution
against taking the estimated position of the QTL too seriously. The confidence
interval is estimated according to Darvasi A and Soller M (1997). A simple
method to calculate resolving power and confidence interval of QTL map location.
Behav Genet 27(2): 125-132.
- The Trait list window now shows the current progeny order for each trait
and the items (loci and other traits) in the background for the trait.
- A new menu under the Progeny menu allows you to create a new sorted progeny
order in a single step.
- Progeny can now be sorted by trait value.
- The speed of the permutation test has been increased by about 40%.
- Import and export functions have been made more versatile. QTX will now
export marker or trait data using a particular progeny order, allowing export
of a subset of data or export of data in a custom order. Second, QTX will
now import or export progeny names from a text file. Third, QTX allows a
choice of characters between genotypes in a text file for import; this change
make it much simpler to import genotypes that have been saved as a text
file from Excel.
- QTX now exports data in a format suitable for pseudomarker (Sen S and
Churchill GA (2001). A statistical framework for quantitative trait mapping.
Genetics 159: 371-387.).
- A new option in interval mapping allows you to suppress the legend in
the interval mapping figure.
ex-features
- Chromosome-specific progeny orders are no longer available. That is, only
one type of progeny order can be created, all progeny order functions work
with type, and all progeny orders are available to all chromosomes. This
change simplifies the use of progeny orders without loss of functionality.
- The permutation test no longer has options for including background loci
during a permutation test. This was an option without a good rationale.
The new Residual function allows creating a trait representing residual
values after fitting a regression with one or more markers representing
QTLs. Using this residual trait in a permutation test will establish an
empirical significance threshold for an additional QTL, as described by
Doerge RW and Churchill GA (1996). Permutation tests for multiple loci affecting
a quantitative character. Genetics 142: 285-294.
- Popup menus in the text find window have been removed. These functions,
for copying or marking chromosomes or loci, did not work properly. Problems
with similar popup menu functions in the find report window have been fixed.
bug fixes
- Marker linkage testing for P=1e-5 and P=1e-6 did not work correctly for
progeny sizes less that 100. This problem also meant that Make Linkage Groups
and Distribute did not work correctly for small datasets and those significance
levels. This problem has been fixed.
- The Statistics window has been fixed to display crossovers for doubled
haploids.
- Option menu items are now disabled when no dataset is active and QT menu
items are now disabled when all traits are removed from a dataset.
- Some problems with highlighting of items in the marker regression report
window have been fixed.
- A problem caused by importing a Mapmaker file with a long file name has
been fixed.
- A blank locus name with be replaced with "NoName" when the file
is saved, to avoid problems when the file is subsequently opened.
- The erratic behavior of the user-defined map distance edit box in the
statistics window has been fixed, and user-defined distances in the locus
edit modal are now displayed consistently in cM.
- Problems caused by attempting to cancel a text import have been fixed.
- In the progeny edit modal, the length of the progeny name is now properly
limited to 5 characters.
- Creation and modification dates in the trait edit modal have been fixed.
- Crashes that have been fixed:
- A crash caused by attempting to print the Notes or Clipboard windows
has been fixed.
- A crash caused by multiple trait mapping with a chromosome containing
only two loci has been fixed.
- An intermittent crash in the permutation test has been fixed.
- Crash caused by closing a label or progeny order dialog while a text
edit box was active.
- About a dozen other minor bugs have been fixed.
version b13 -- 9/26/01
new features
- The QT Links report has a button to allow you to add a selected locus
in the report directly to the background of the trait, in preparation for
composite interval mapping.
- The Stat window can now be saved as a text file.
- Trait values can now be exported as a text file.
- A function for detecting epistatic interactions is written but is inactive
pending further testing.
ex-features
- The Fast Interval Mapping function has been removed. This has always been
considered an experimental function. There have been some unresolved questions
about the implementation, and recently a question has arisen concerning
its theoretical basis. The speed of interval mapping is generally great
enough that this function offered no compelling advantage.
bug fixes
- Fixes the map distance problem introduced in b12 for recombinant inbred
data.
- Changed the routine that eliminates trailing spaces in locus names to
allow internal spaces in the names.
version b12 -- 8/16/01
bug fixes
- Fixed multiple problems with printing the Phenotype, Map, Statistics,
and Reference windows, expecially problems with pages after the first when
the printout extended over multiple pages.
- Fixed interval mapping with user-defined map distances.
- Changed locus name storage to eliminate trailing spaces, which could cause
problems in importing data or pasting data from another set.
- Fixed a crash that could occur when adding a new locus after adding new
progeny to a set.
- Fixed the haplotype sort, which failed to sort nonrecombinant progeny
by genotype.
- Fixed a crash which often occurred when closing the progeny order window
after making a new progeny order.
- Fixed two crashes which sometimes occurred when trying to cut or copy
progeny.
version b11 -- 5/16/01
new features
- Added a "Reverse locus order" item to the Locus menu. This reverses
the order of a selected group of loci or, if no loci are seleced, of all
the loci in the active chromosome.
- The total map length of a chromosome is now displayed in the header of
a chromosome list window.
bug fixes
- The mouse pointer watch symbol was changing back to an arrow during a
lengthy Distribute test, making it appear that Map Manager had crashed.
It now remains a watch symbol.
- In data exported in QTL Cartographer format, map distances are now always
included and they are expressed in cM rather than M.
- Fixed a problem with saving and reading traits if no trait values were
entered for parental individuals.
- Fixed an apparent crash when attempting to use background loci for interval
mapping of a trait which had not background loci defined. This was not a
real crash, but the alert window which reported the lack of background loci
was taking so long to close that it appeared to have crashed. Changed the
window type for that alert and other similar alerts.
- Fixed many memory leaks during the permutation test which would cause
Map Manager to run out of memory during a lengthy permutation test.
- Fixed a crash when attempting to export to Mapmaker format with the "Allow
mixed segregation types" option unchecked.
version b10 -- 3/29/01
new features
- Map Manager now has facilities to define fixed map distances for one or
all intervals between marker loci. In the Statistics window, if you double-click
on a map distance, you will open an edit box that allows you to enter your
own map distance. When you press Enter/Return, the edit box will accept
your number and move to the interval below. You can quickly move through
the whole chromosome, entering distances as fast as you can type. These
user-defined map distances will be used as long as the loci are in the original
order. If you rearrange loci, Map Manager will calculate map distances for
the new intervals created. If you return loci to the original order, it
will again use the user-defined distances.
- When exporting marker genotypes in text file, Mapmaker, Cartographer,
or QGene format, Map Manager now respects the setting of the Show Inferred
option. That is, when Show Inferred is on, Map Manager exports inferred
genotypes as the inferred value; when it is off, Map Manager exports inferred
genotypes as unknown.
- Map Manager has a new function to hide loci which are redundant for the
purposes of QTL mapping. If two loci have the same location (they are not
separated by at least one recombination event), this function will hide
one of them, preferentially hiding the least informative.
version b09 -- 2/11/01
new features
- Interval mapping for multiple traits simultaneously, with a display for
comparing location of the QTLs for these traits.
bug fixes
- Fixed a crash when deleting an item from the background of a quantitative
trait.
version b08 -- 9/25/00
bug fixes (thanks to the bug detection of intern Jessica Kocsis)
- Fixed a crash when clicking the close box on the Mapmaker export dialog.
- Fixed a crash when exiting the program with multiple Find Report windows
open.
- Fixed a crash when exiting the program with Find, Notes, or Clipboard
windows open.
- Fixed a crash when choosing Window->Close with multiple windows open
including at least one Clipboard, Notes, or Permutation Report window.
- Fixed a crash when clicking OK in the Preferences dialog with on dataset
open.
- Fixed a crash when choosing Window->Close with no window open.
- Fixed a crash when closing a dataset with Find Report windows open.
- Fixed a crash when dragging chromosomes or loci between datasets when
one or the other is not displaying the Internal progeny order.
- Fixed a crash when dragging a trait to the desktop.
- Fixed an corrupted data file when saving a data file after cutting progeny.
version b07 -- 8/18/00
new features
- Added linkage and search criteria of P = 1.0e-5 and P = 1.0e-6. These
stringent linkage criteria are useful when creating linkage groups with
large datasets (that is, hundreds of loci).
bug fixes (thanks to the bug detection of intern Jessica Kocsis)
- Several bug fixes which improve the accuracy of Make Linkage Groups, that
is, which improve its ability to create the proper number of groups.
- Fixed a bug which could cause crashes during any QT analysis if the dataset
contained unknown genotypes.
- Fixed several problems with printing.
- Fixed problems with the Reset function in the Set Edit and Preferences
modal windows.
- Fixed the automatic generation of non-numeric progeny names, that is,
those that begin with one or more letters.
- Fixed the loss of trait information when progeny are copied, cut, or pasted,
or when those editing operations are undone.
- Fixed crash when trying to hide chromosome with no chromosome selection.
- Fixed crash when trying to cut chromosome trait from trait list with trait
window open.
- Fixed crash when trying to save window if the window was a map window
or graphical QT mapping window
- Fixed about 13 other miscellaneous bugs
version b06 -- 6/16/00
new features
- You can now control the visibility of unlabelled loci in the same way
that you could control the visibility of loci marked with a label or a combination
of labels.
bug fixes
- Fixed quantitative trait analysis functions that did nothing for advanced
backcross.
- Fixed a problem with the calculations for weighed regression.
- Fixed a problem with text import caused by an uninitialized radio button
in the dialog.
- Fixed a crash during Make Linkage Groups (Windows only).
- Fixed several problems with Edit commands (Cut, Copy, Paste) applied to
progeny in different progeny orders.
version b05 -- 5/25/00
new features
- Map Manager now has the ability to do weighted least squares regression.
This feature may be useful with recombinant inbred lines or other situations
where trait values can be measured for multiple genotypically identical
individuals. To use this feature, measure several individuals from each
RI line for the trait and calculate a variance. Enter the variances for
all lines as a separate trait. In the QT Links or Interval Mapping dialog
box choose that trait from the new popup menu as the one which has trait
variances.
- The header of the Phenotype window now lists the total number of crossovers
in the chromosome. This total does not include crossovers whose position
is ambiguous because of missing data.
- Locus labels can be included in text file exports and are accepted in
text file imports.
bug fixes
- Fixed crash occurring when the dataset was edited while a chromosome window
was open.
- Fixed a missing keyword in the header of an exported Mapmaker file.
version b04 -- 4/21/00
bug fixes
- The permutation test report now includes the empirical p-value if one
is requested.
- The number of decimal places displayed in the trait edit dialog is reduced
to improve readability.
- Labels for new progeny now default correctly to none.
- Unknown phenotypes are now inserted where necessary for progeny pasted
into another dataset.
- The order of a group of chromosomes is now preserved when it is dragged
into another dataset.
- QTL mapping now works for doubled haploid populations.
version b03 -- 2/28/00
new features
- File>Import>Trait text imports a text file of trait values.
- File>Save Window will now save the Map window as a graphic file.
- The QT>Transforms submenu now has items for creating a trait which
is the sum, difference, or product of two traits.
bug fixes
- Fixed crash while mapping QTLs in a dataset which has a chromosome with
only one locus.
- Fixed modification of unknown trait values during saving and reopening
files (Windows version only).
version b02 -- 2/15/00
new features
- Export marker data, trait data, and map data in QGene format.
- Print report windows.
- New menu item, Save Window, allows saving report windows in a text or
graphics file.
bug fixes
- Fixed crash while exporting to QTL Cartographer format.
- Fixed data conversion problem occurring when opening Map Manager QT files
containing backcross data.
version b01 -- 2/7/00
Map Manager / Ken Manly / mapmgr@roswellpark.org