Software

J/qtl Software Change History

 

Version 1.1.1, July 14, 2008

This is a minor bug-fix only release.

Minimum Requirements:

  • The memory requirement depends on the size of the input data but a minimum of 512MB memory is recommended.
  • Operating System: Windows XP, Windows Vista or Mac OS X 10.4 or greater
  • R 2.7.0 or greater
  • R/qtl 1.08 or greater (J/qtl will attempt to install this for you if it is not already installed)
  • Java 5.0 or greater

Issues Fixed:

  • Wrong phenotype label was being used in scan results and scan graphs in some circumstances (single trait scans not using the first phenotype).

Improvements:

  • No other improvements

Known Issues and Limitations (to be corrected in a future release of J/qtl):

  • Crosses (and other data objects) cannot be deleted or renamed in a project
  • J/qtl does not yet check that new data object names are different than existing ones. Please be sure to give your data objects unique names until we implement this.
  • Data object ordering is not completely consistent throughout the application

Version 1.1.0, June 14, 2008

This is a minor release that includes some enhancements requested by J/qtl users as well as a couple of bug fixes.

Minimum Requirements:

  • The memory requirement depends on the size of the input data but a minimum of 512MB memory is recommended.
  • Operating System: Windows XP, Windows Vista or Mac OS X 10.4 or greater
  • R 2.7.0 or greater
  • R/qtl 1.08 or greater
  • Java 5.0 or greater

Issues Fixed:

  • Fixed bug that caused load cross to fail when a cross file contained N/A categorical phenotypes
  • Fixed bug that caused incorrect colors to be rendered in the RF plot when not all of the chromosomes are selected

Improvements:

  • J/qtl now allows the user to include multiple phenotypes in a One QTL or Two QTL Scan
  • J/qtl now remembers: previous 10 project files, last image export directory, last R script export directory, last export table directory
  • Most graphs allow user to zoom and translate the X & Y axis. The phenotype histogram plot also allows the user to modify bin size
  • "Save Image" capability is now available for all graphs
  • Added confirm on close dialog that prompts the user if there are any unsaved project changes

Known Issues and Limitations (to be corrected in a future release of J/qtl):

  • Crosses (and other data objects) cannot be deleted or renamed in a project
  • J/qtl does not yet check that new data object names are different than existing ones. Please be sure to give your data objects unique names until we implement this.
  • Data object ordering is not completely consistent throughout the application

Version 1.0, May 30, 2008

Minimum Requirements:

  • The memory requirement depends on the size of the input data but a minimum of 512MB memory is recommended.
  • Operating System: Windows XP, Windows Vista or Mac OS X 10.4 or greater
  • R 2.7.0 or greater
  • R/qtl 1.08 or greater
  • Java 5.0 or greater

Major Improvements:

  • Created a Java WebStart installer for simplified deployment
  • Improved application help files
  • Added QTL model fitting with formula editor
  • Added an R command preview panel to most dialogs that cause an R command to be issued
  • Added "Simulate Cross" functionality
  • Improved project save/load functionality
  • Created non-blocking R interface that allows for user interaction and feedback while R/qtl is busy
  • Improved One and Two QTL Scan interface
  • Added data preview to the load cross dialog
  • Added interactive confidence intervals and alpha thresholds to the One QTL Scan Plot
  • Added support for multiple crosses

Version 0.9, Dec.26th, 2006

Modification history: 

 Dec. 28th, 2006 - for fixing bug 3.
 Jan. 19th, 2006 - for fixing bug 4 and adding major improvements 6.
 Feb. 26th, 2007 - for adding major improvements 7.
 Feb. 28th, 2007 - for fixing bug 5.
 Apr. 2nd,  2007 - for fixing bug 6 and 7.

Corresponding R and R/qtl version: 

  • R/qtl: 1.05
  • R-2.4
Major improvements:
  • Modified the summary and display functions to display the new scantwo and scanone result of R/qtl.
  • Increase the default R memory limit on Windows Machine to 2 GB.
  • Added "Save QTL Basket" button on "QTL List" page.
  • Added feature for accepting datasets with categorical pheno type.

    • J/qtl convert the categorical pheno type data in original data file and save to a new data file as "originalFileName-jqtl.csv".
    •  Value in Sex column is converted to 1 or 0 for male or female if they are not numerical. Any word starting with "m" will be converted to "1", and anything starting with "f" will be converted to "0".
    • If user data has pgm column, data in that column has to be numerical.
  • Added "about" page for the software
  • Added the checking for sex and pgm column existence in data file if X chromsome exist. If it's not, ask user to modify their data first.
  • Added the feature to start Rserve on different Mac architecture, namely ppc and i386.

Bug fixes:
  • Bug: loading error when a chromosome has only one marker.

    This is fixed.

  • Bug: If I run a calculate genotype probabilities at 2 cM and then rerun the "One QTL SCan" it gives an error message if I try to generate an effect plot for the calculated genotypes but it does give a correct effect plot for the DMit Marker.

    This is fixed by lunching a 16-page imputation following the "calculate genotype probabilities". If the user has done more than 16 pages permutation, J/qtl will ask user to confirm if they really want to do it.

  • right click on scanone result plot doesn't work on Mac.

    This is fixed by switching to left click

  • When the sex column name is in lower case "sex", Jqtl cannot recognize it as sex column.

    This is fixed. Jqtl can accept any combination of capital/lower case of "sex" and "pgm".

  • Cannot print or save image for the multiple scanone plot.
    This is fixed.

  •  Bug: Cannot plot histogram for some pheno type.
        This is fixed.

  •  Bug: When phenotype has missing, Jqtl complains non-numerical value  in phenotype data. This is incorrect.
        This is fixed.


Known limitation for this version:
  • user needs to manually convert pgm column to numerical coding.
  • not all R/qtl functions are included.
  • not all R/qtl funcion options can be accessed from J/qtl.
  • combined cross is not implemented in this version.
  • only one cross can be in workspace.

Version 0.8, 5/10/2006

Initial release. Currently all the basic analysis tools were implemented including:

  • Visualization of genotype data, genetic map, recombination fraction, phenotype data
  • One- or Two-QTL genome scan with plot and summary
  • Higher-order QTL model building and scanning

We will develop a phenotype viewer as a (kind of) separate program to visualize, transform and do basic analysis on phenotypes.