Download FLOSS files
- Executable files
- Sample input and output files
- R script for graphing
- FLOSS and COV source code
- FLOSS version notes
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Executable files
The floss.jar and cov.jar files can be executed
with a java interpreter (version 1.4 or later)
using the "-jar" option.
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Sample input and output files
The following sample files show the input and output files used to
run an ordered subset analysis using MERLIN, COV, and FLOSS.
- Merlin files
- MERLIN data file.
The data file
is used MERLIN to create the .lod file and by the COV program
to create the covariate file with family covariate scores.
- MERLIN pedigree file.
The pedigree
file is used by MERLIN to create the .lod file and by the COV program
to create the covariate file with family covariate scores.
- MERLIN map file. The map
file is used by MERLIN to make the .lod file.
- MERLIN .lod file. The .lod
file contains the family LOD scores at each locus
and is used by FLOSS to carry out an ordered subset analysis.
The .lod file was
created by MERLIN using the pedigree, map, and data files with
the command:
merlin -d test.dat -p test.ped -m test.map -ff --npl
--grid:2 --perFamily
- Covariate file. The covariate file
gives the family covariate score for each family and for each
covariate, and is used by the FLOSS program to
order families by their covariate value.
The covariate file was created by the COV program with the
command:
java -jar cov.jar -d test.dat -p test.ped -o test.cov
- FLOSS output files.
The output files were created by the FLOSS program with the command:
java -jar floss.jar -c test.cov -merlin merlin.lod -o floss.test --npl
Download all input and output sample files
as a .zip file.
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R Script for graphing ".plt" file linkage scores
The plot.r script
will graph the linkage scores in the plotting (.plt) files generated
with FLOSS version 1.4.1 or later. Documentation for plot.r
is included in a comment at the top of the R script.
R is a free statistical software package available from
http://www.r-project.org.
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FLOSS and COV source code
Download source code for FLOSS and COV as a zip file
After extracting the *.java and *.mf files from the
zip file to a folder named "floss", switch to the "floss" folder, and
compile the COV and FLOSS executables with the commands
javac -source 1.4 *.java
cd ..
jar -cvfm floss/cov.jar floss/cov-meta-inf.mf floss/*.class
jar -cvfm floss/floss.jar floss/floss-meta-inf.mf floss/*.class
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Version Notes
The version notes describes improvements
that have been added to FLOSS since its public release.
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