major bug fix
- Map Manager no longer loses, during file saving, any reference or comment exactly 255 characters long.
new feature
- The QGene export function now has an option for doubled haploid populations.
- The trait data entry dialog has "=Prev" buttons beside the reference and comment fields which will enter into the field whatever was entered for the preceding trait.
minor bug fixes
- The width of the figure copied from the map window has been increased ten-fold to avoid truncating information on the right side of the figure.
major bug fixes
- When opening a data file, Map Manager QT no longer scrambles some trait data which contains untyped values.
- When saving a data file, Map Manager QT no longer scrambles inferred marker typings. This bug was recently introduced in the course of other changes.
minor bug fixes
- Increased the maximum line length for importing trait data from a Mapmaker file.
new features
- The speed of the permutation test has been improved by about five-fold (dependent on the machine and Mac OS version).
- A new function, Ripple, has been added to the Goodies menu. This function tests local permutations of loci in a selected chromosome to try to improve the locus order. The order is evaluated by summing the LOD scores for linkage of all adjacent pairs of loci, and Ripple attempts to maximize this sum. The Distribute... function also uses Ripple to optimize locus order as it adds loci to destination chromosomes.
major bug fixes
- Map Manager QT will now properly import files from Map Manager XP, the cross-platform version of Map Manager. Use File>Import>Untyped to open files transferred from the Windows version of Map Manager XP. File>Open will also work, but the file willl appear in the open dialog only if the Macintosh file type has been set correctly. Until we release a Macintosh version of Map Manager XP, you will be unlikely to have files with the correct file type. The coding conventions for backcrosses are different for Map Manager XP and Map Manager QT, but Map Manager QT will translate the phenotypes when it imports a Map Manager XP file.
Version b25 was released only at The Jackson Laboratory. Features are included in the description of b26, above.
new features
- The Distribute... function can now be interruped by Command-period.
major bug fixes
- Fixed crashing of 68K version which occurred in various places when it handled trait data.
new features
- A new function, Distribute..., has been added to the Goodies menu. This function will distribute loci from a selected chromosome to their best positions in a selected range of chromosomes elsewhere in the dataset. The best positions are defined by the greatest increase in LOD for linkage. This function is intended to aid the placement of large numbers of new loci in existing datasets. The function calculates the increase in LOD score for all possible moves, moves the locus which results in the greatest increase, then recalculates affected scores before moving the locus which results in the next largest increase. Any locus which is not linked to one of the flanking loci at the destination location is not moved. In addition, the user can specify a minimum LOD increase; any locus which does not meet this minimum is not moved. The function creates a report which lists the destinations and the increase in LOD score for each locus moved.
- As a side effect of creating the Distribute command, the method for the Find Best command has changed. Find Best now evaluates placement according to the increase in LOD for linkage, like the Distribute command. This should make it more reliable in datasets with unknown typings.
- A new report has been added to the Reports menu. This report creates a simple table, for radiation hybrid data, which lists the number of fragments of each size in each cell line, where size is measured by the number of adjacent markers carried by the cell line.
- Closing a dataset window now closes the dataset. That is, closing the dataset window will prompt to save changes, if necessary, and then remove the dataset from the computer memory so that it is no longer available. The dataset window is the window which lists the chromosome names and the number of loci and linkage groups in each chromosome. In previous versions, closing the dataset window would leave the dataset in memory, still available as an item in the Set menu. However, users found this confusing because, unless they specifically looked for it in the Set menu, there was no visible indication that the dataset was open and available.
- The command which makes all hidden loci in a chromosome visible, formerly called Show All, is now called Unhide All and can be invoked using the key equivalent Command-U.
- This version of Map Manager QT can now read data files from Map Manager XP, the cross-platform (Microsoft Windows and Mac OS) mapping program.
major bug fixes
- Fixed a bug which prevented or affected composite interval mapping or permutation tests when some progeny were untyped for the background markers.
minor bug fixes
- Fixed a bug which prevented copying and pasting loci within datasets with exactly 32 strains.
- Fixed a bug which generated absurd map distances for radiation hybrid data having adjacent markers with large numbers of discordant typings.
- Fixed a bug which displayed absurd map distances in the Statistics window when adjacent markers were unlinked.
- Fixed a recent bug which prevented reading files from Map Manager Classic.
- Fixed a bug which prevented selecting a locus in a chromosome list window (a phenotype, statistics, or reference window) by typing its name. Now you need not type the whole name. Map Manager will highlight the first locus for which the beginning of the name matches what you have typed. Typing <return> or <enter> forces the search to start immediately, but in any case it will start automatically after a pause in typing. A reminder--once you have selected the locus, you can open the editing window by typing <command>-<return>.
Version b22 was released only at The Jackson Laboratory. Features are included in the description of b23, above.
new features
- Added a field to the permutation dialog which allows the calculation of an empirical probability estimate for a likelihood ratio value chosen by the user. This allows you to estimate the probability of a specific LRS value obtained from interval mapping.
- Raised the maximum number of background loci for composite interval mapping from seven to sixteen.
major bug fixes
- Fixed three bugs in the permuation test function. My statistical collaborator, Jane Olson at Case Western Reserve, recently convinced me that my implementation of the permutation test in Map Manager QT was faulty. I had changed the order of calculations from that originally described by Churchill/Doerge in an attempt to make the calculations faster. I have now rewritten the permutation test to match the original description. In the course of rewriting, I discovered and corrected two other problems which affect version b20 and probably other recent versions (I am not sure how many).
minor bug fixes
- Fixed a problem which displayed a large map distance for radiation hybrid data when the distance was, in fact, undefined.
new features
- Map Manager QT now exports dataset in QTL Cartographer format, creating two files, one with marker map and one with marker genotypes and trait phenotype information. These are in the proper format to be processed by Rmap and Rcross, respectively.
- Map Manager QT now accept ambiguous or uncertain radiation hybrid data. In the dataset editing dialog, you can define single-letter abbreviations for uncertains positive data (+?) and uncertain negative data (-?). The Linkage Evaluation submenu (Option menu) now contains three radiation hybrid settings. The first treats all uncertain data as negative. The second treats uncertain postive as positive and uncertain negative as negative. The third treats all uncertain data as positive.
- A new commmand, Recite SDP, appears when the Speech Manager is available. This allows the computer to read audibly the abbreviations of the phenotypes for a selected locus. In version b1968K this command appeared in the menu but if it worked at all it spelled the locus name rather than reading the SDP. If your system software predates version 7.6, you may need to install text-to-speech software available from Apple Computer.
- It is now possible to Infer or Flip Phase for a range of loci. The Flip Phase item is now active when a range of loci is selected but not when a range of chromosomes is selected.
- A new command, Reverse Order, which will reverse the order of a selected range of loci, appears in the Locus menu.
major bug fixes
- Fixed bug in Save code which caused a new dataset to appear to be saved when in fact it was not.
- Fixed some cases in which command-period did not halt a lengthy procedure as it should have.
minor bug fixes
- Removed an extra line preceding progeny information in the data file format. This should have no effect on file reading or saving.
major bug fixes
- Import of references and comments now works properly.
- Trait import now accepts numbers larger than 32767
- Trait import now reads last trait in the file even if it is not terminated with a carriage return character.
minor bug fixes
- Dialog is now properly removed when user cancels a QT Transform operation.
- Menubar flashing is fixed.
major bug fixes
- Saving a data file now saves progeny display orders instead of trashing them.
- Behavior of popup menus in Make Order Internal dialog is fixed.
- Make Order Internal now rearranges order for trait values as it rearranges marker phenotype orders.
- Details report works again--was broken during changes for PowerPC version.
minor bug fixes
- Cutting, pasting or clearing progeny now flag a dataset as being changed and needing to be saved.
bug fixes
- A inaccuracy is fixed in the % explained value of QT links report and interval mapping reports.
- The links report and interval mapping report now agree on the regression coefficient for QTLs in recombinant inbred lines. In the previous version, these values differed by a factor of two.
- The sign of the regression coefficient in the QT links report now agrees with that in the interval mapping report in all cases.
features
- The permutation report now includes the start and finish times.
- The new trait routine now supplies a default name for a trait if not provided by the user. This prevents subsequent misbehavior of menus which list trait names.
major bug fixes
- Define Text for Find... now works, instead of failing to open the dialog or crashing.
- The Rearrange dialog no longer crashes the PPC version.
- The scrolling genotype list in the locus editing dialog once again displays all six characters of long progeny names.
- The Mapmaker import and GMendel import dialog boxes no longer crash the PPC version.
- Map distances stored by the QGene export routine for unlinked markers have been corrected.
- Adjacent loci with identical genotypes no longer halt interval mapping or permutation tests (or, to be more exact, one cause of such halting has been fixed).
features
- All the commands under the Locus / Hide Multiple submenu will now act on a range of selected chromosomes.
- The Locus / Show All, Locus / Infer, and Locus / Swap commands will now act on a range of selected chromosomes. If the option key is held down, the Locus / Show All command will act on all the chromosomes in the dataset.
major bug fixes
- Fixed a bug causing a crash when editing a locus in the PowerPC version.
- Fixed an inconsistancy in the display of linkages in radiation hybrid datasets.
- Fixed the Locus / Hide Multiple / Public command so that it will apply to all chromosomes only when the option key is held down.
features
- Limited support for radiation hybrids (see below)
- A PowerPC native version!!! Separate versions are now available for 68K and PowerPC Mac OS. On a PowerPC Mac, the native version appears to be about two-fold faster in the permutation test. Producing the PowerPC version required extensive internal changes in the code. In principle, these are not supposed to alter the behavior of the program. However, if they do cause a change, the change could also appear in the 68K version, because both versions are produced from the same code files.
- A new hypertext manual which covers both Map Manager Classic and Map Manager QT. This manual, which consists of almost 200 files, is available as a single stuffed archive for those who want to install it on local computers. A frames-aware browser (Netscape Navigator 2 or better) is recommended.
major bug fixes
- Fix printing problems: checkboxes in the print dialog were not controlling the options they should have been controlling, and cumulative map distances in a printed map were wrong if the map extended to a second page.
features
- Add limited support for radiation hybrids. This enhancement adds a "Radiation Hybrid" option to the Linkage Evaluation submenu. When this item is checked, Map Manager QT treats progeny as radiation hybrid cell lines. For any locus, the "maternal" allele is interpreted as indicating presence of the locus in a line; the "paternal" allele, as absence. All other alleles are treated as "unknown". The display in the SDP window is changed to emphasize contigs, and linkages and distances are calculated as described by Cox and coworkers, Science 250: 245-250 (1990).
other changes
- Convert to version 10 of the CodeWarrior development system. In principle, this should make no difference in the behavior of the program...
minor bug fixes
- Fix a problem with opening files of Map Manager Classic. this bug was introduced by the switch to CodeWarrior 10 (see above).
minor bug fixes
- Fix crash when trying to add progeny to a dataset with fewer than 48 progeny.
features
- A new addition to the to the Chrom/Apply Progeny Sort menu, which allows you to sort progeny by trait value. This will be very useful to those wanting to genotype only those progeny which have extreme trait values. Most useful in connection with the next item.
- An enhanced QT/Align command, which now allows you to align a trait window with any chromosome or locus. This is important because trait values are not displayed in sorted order unless the trait window is aligned with a chromosome. (Progeny orders are specific to individual chromosomes, and traits are not intrinsically identified with any one chromosome.) If you want to display trait values in sorted order, sort a chromosome by the trait and then align the trait window with a locus in that chromosome.
major bug fixes
- Fixed interval mapping with background loci, which always failed and suggested hiding loci which, in fact, did not need hiding. This had been broken by the extensive revision leading to the better permutation test (b9).
- Fixed the QT Find command, which did not do anything. This was another casualty of the better permutation test.
other changes
- Add description of background chr and loci to permutation report and report distribution of LRS values in bins of 0.2 instead of 1.0.
- Changed the new set dialog to make it clear that progeny names cannot be changed until the dataset is created. This restriction is imposed because changing the number of progeny in the new set dialog (which is easy) instantly discards any custom progeny names.
minor bug fixes
- Fix sorting by crossovers which failed to distinguish singly and doubly for F2 populations.
- Fix a bug which caused the sign of the regression coefficient to be different for a QT Links report and for an interval mapping of the same data. This only affected backcross populations in which the maternal trait value entered in the QT edit window was higher than the paternal trait value. This bug, in effect, reversed the interpretation of maternal and paternal for background loci only (not the target interval) in those populations. This bug did not affect datasets in which no values were entered for the parental trait values.
major bug fix
features
- A better permutation test -- The permutation test is rewritten so that it only uses progeny which have a trait value. This means that you can now do a permutation test on a set which has missing trait values and (1) the test will not fail and (2) the thresholds will be accurate. This change should probably be listed under bug fixes, but it is important enough to be listed first.
- Both interval mapping and the permutation test will now report the locus and chromosome at which a regression error occurs. This will allow you to diagnose the error or remove the offending locus.
just plain changes
- The modifier key for the Locus Uninfer menu item has been changed from Command to Control. This was necessary because the Infer menu item had been given a command key equivalent.
- In the interval mapping figure, there is now a minimum scale factor of 15 for the likelihood ratio statistic. This will prevent to program from scaling insignificant statistic values so that, at first glance, they look significant.
- The spacing of columns in the haplotype figure, which was greatly reduced in a previous revision, has been increased slightly to separate the numbers at the bottom of the columns.
major bug fix
- Fixed loss of locus alias names when reading a Map Manager QT file. QTb8 (and probably all previous versions) fail to read the alias name when opening a Map Manager QT fail. However, b8 does read alias names when opening a Map Manager Classic file and it does save alias names. Thus, when you first open a Map Manager Classic file and save it as a Map Manager QT file, the alias names will be intact. If you then open the Map Manager QT file, make a change, and save the file again, all alias names will be gone. Since the alias names only appear in the locus editing dialog, the loss can be undetected for quite a while. If this loss has affected you, email me; I have written an AppleScript program which may be able to restore the alias names from an unaffected Map Manager Classic file.
bug fixes
- Fix the calculation of "% variance explained", which appears in the QT Links Report and in the Interval Mapping Report. This is the figure under the "%" heading in both of those reports. In verson b8, this figure was much larger than it should have been. It is now corrected and it is also now affected by the checkbox labelled "Evaluate primary association only" or "Evaluate interval QTL only". When this box is checked (the default) the "% variance explained" does not include the variance explained by background QTLs. When the box is unchecked, it includes the variance explained by all QTLs in the analysis.
- The viewing width of a chromosome map window has been tripled to avoid cutting off long strings of locus names.
- Fix a bug in the "Omit confidential" checkbox in the Save As... and Export... dialogs which caused it to work backwards if it was clicked. That is, if it was not clicked, it would correctly indicate that confidential information was included. Once it was clicked at least once, it would indicate the opposite of what the program would do.
- Fix a bug which caused the trait name to be omitted from the interval mapping figure.
- Fix highlighting which was black instead of the system highlight color.
- Fix a bug in the Locus Reinfer command; it failed to reinfer correctly if there were several inferred loci in a row.
features
- The big new feature for b8 -- for QT Links Report, Interval Mapping, and Permutation Test with intercross data, add the option for specifying a regression model which is one of the following: free, additive, dominant, or recessive. Under the free model, Map Manager QT fits two regression coefficients, one each for an additive and a dominance component. For the other models (constrained models), Map Manager QT fits only one coefficient, assuming that one allele of the QTL is additive, dominant, or recessive, respectively.
- Add a column to the QT Links Report and to the Interval Mapping Report which gives the percentage of the variance which is explained by the QTL bein mapped (thanks to Wayne Frankel).
- For Interval Mapping Report and Interval Mapping Figure, create a default file name which contains the trait name and date following either "IMR" or "IMF", respectively (thanks to Rob Williams).
- Make the Permutation Test store its results in a file (thanks again to Rob Williams).
just plain changes
- Change the operation of the =Prev button in the locus editing dialog so that it retains the confidential part of the reference or comment (thanks to Lucy Rowe).
- Make the QT Links Report window wider and change the report so that small P values are displayed in exponential notation instead of sometimes being displayed as 0.00000 (thanks to Rob Williams).
bug fixes
- Find a work-around which may fix the "invisible interval mapping figure window syndrome". This has been a frustrating bug manifesting itself as a failure to display the interval mapping figure when interval mapping is run for the the second (or Nth) time. The bug could be avoided by closing the first mapping figure window before running the routine again. The work-around makes no sense, but since it seems to work, I will leave it in the program and look forward to feedback from those who have encountered this bug.
- Fix error which affects calculation of additive component of regression coefficient, effectively using the wrong mapping function. Probably not noticeable for distances less than 10 cM.
- Rewrite the interval mapping functions for recombinant inbred lines to allow for heterozygotes. This assumes heterozygotes are a small minority and always uses a constrained additive regression model.
- Change the "Suggestive" cutoff calculated by the Permutation Test, making this cutoff significantly less stringent (thanks to a challenge from Rob Williams for uncovering this error).
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