home </home>


    Source code for PGA Grid, ver. 1.01

PGA Grid is an HTML-based system created for displaying results of
large-scale *P*henotype-*G*enotype *A*ssociation studies. It was
developed under the auspices of NHLBI's CardioGenomics Program for
Genomic Applications <http://www.nhlbi.nih.gov/resources/pga/index.htm>.
Each grid packages the results of a large number of association tests in
such a way that strengths of associations are interpretable at a glance,
while at the same time making the supporting data available easily in
the form of graphs that can be accessed at the click of a mouse.

The source code is written for our platform of a Red Hat Linux machine
running AOLserver <http://www.aolserver.com> v3.4.2, Oracle
<http://www.oracle.com> 8i, and the ArsDigita Community System
<http://www.eveandersson.com/arsdigita/acs-repository/> web toolkit,
v3.2.0 (docs </doc/index.html>). Graphics-drawing tools required are
Thomas Boutell's GD <http://www.boutell.com/gd/> (we use Spencer
Thomas's Tcl interface to GD, gdtclft <http://www.graphviz.org/>), and
ChartDirector <http://advsofteng.com/>.

Version 1.01 of PGA Grid was customized to the particular requirements
of the first CardioGenomics association project (between left
ventricular echocardiographic phenotype and SNP genotype). As such, this
source code is provided primarily as a reference rather than as a
standalone software application. Future versions will be more
generalized to allow flexibility in choice of parameters. The most
recent version of this software can be found at
http://cardiogenomics.med.harvard.edu/src/pga-grid/.

Note that association statistics are calculated beforehand; these pages
only display precalculated numbers. The file
pg-input-sample-primary1.txt is a tab-delimited text file containing a
simulated sample of the input data. This sample file is processed by a
Perl script, process-pvalue-spreadsheet-sql.pl
<process-pvalue-spreadsheet-sql.pl.txt>, to create .sql files to update
database tables.

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      The files

assoc-results.tcl </projects/p5/assoc-search.tcl>
    Presents display choices for viewer: Display gene-list, display all
    thumbnails, or search for low pvalues. A good place to start
    viewing. /(view source <assoc-results.tcl.txt>)/
assoc-gene.tcl </projects/p5/assoc-gene.tcl?gene=AGTR1>
    Displays PGA Grid thumbnails for all SNPs in a given gene. (/view
    source <assoc-gene.tcl.txt>/)
assoc-search-2.tcl </projects/p5/assoc-search-2.tcl?pvalue=0.001>
    Displays results of search-by-pvalue, with grid thumbnails. (/view
    source <assoc-search-2.tcl.txt>/)
assoc-all-icons.tcl </projects/p5/assoc-all-icons.tcl>
    Displays all Primary PGA Grid thumbnails (icons) in all genes, on
    one page. (/view source <assoc-all-icons.tcl.txt>/)
gei-all-icons.tcl </projects/p5/gei/gei-all-icons.tcl>
    Displays all Gene-Environment Interaction grid thumbnails in all
    genes, on one page. (/view source <gei-all-icons.tcl.txt>/)
assoc-grid-frame.tcl </projects/p5/assoc-grid-frame.tcl?snp_id=86>
    Frameset for assoc-grid.tcl and lsm-graph.tcl. (/view source
    <assoc-grid-frame.tcl.txt>/)
gei-grid-frame.tcl </projects/p5/gei/gei-grid-frame.tcl?snp_id=86>
    Frameset for gei-grid.tcl and gei-graph.tcl. (/view source
    <gei-grid-frame.tcl.txt>/)
assoc-grid.tcl </projects/p5/assoc-grid.tcl?snp_id=86&frame=1>
    Creates Primary PGA Grid as HTML table, with hyperlinks to bar
    graphs of supporting data. Top frame in a frameset. (/view source
    <assoc-grid.tcl.txt>/)
gei-grid.tcl </projects/p5/gei/gei-grid.tcl?snp_id=86&frame=1>
    Creates PGA Grid as HTML table, for Gene-Environment Interaction
    associations. Top frame in a frameset. (/view source
    <gei-grid.tcl.txt>/)
lsm-graph.tcl
</projects/p5/lsm-graph.tcl?snp_id=86&sample=f&covars=ahwkSDH&model=add&pheno=LVID6>
    Creates and displays bar graph in frame under assoc-grid.tcl. Bottom
    frame in a frameset. (/view source <lsm-graph.tcl.txt>/)
gei-graph.tcl </projects/p5/gei/gei-graph.tcl?assoc_id=488>
    Displays bar graph in frame under gei-grid.tcl. Bottom frame in a
    frameset. (/view source <gei-graph.tcl.txt>/)
cgi-bin/gei-graph.pl
    Perl CGI script that creates bar graphs which are called by and
    displayed by gei-graph.tcl. (/view source <gei-graph.pl.txt>/)
stats/assoc-gene-list.tcl </projects/p5/stats/assoc-gene-list.tcl>
    Ranks genes by a significance metric, to identify genes with the
    most interesting p-values. (/view source <assoc-gene-list.tcl.txt>/)
stats/pv-dist.tcl
</projects/p5/stats/pv-dist?grid=pri&gene=AGTR1&pheno=all&sample=all&model=all&covar=all&snp_type=all&order=pri%5fscore&p_limit=0%2e01&show_allbars=1>

    Displays graph and table showing distribution of p-values for SNPs
    in a gene, according to various user-set criteria. (/view source
    <pv-dist.tcl.txt>/)
cgi-bin/pv-dist.pl
    CGI script that uses ChartDirector to draw a graph for pv-dist.tcl.
    (/view source <pv-dist.pl.txt>/)
tcl/p5-defs.tcl
    Tcl procedures to support Project 5 (i.e. Primary PGA Grid) pages.
    (/view source <p5-defs.tcl.txt>/)
tcl/p5-graph-defs.tcl
    Tcl procedures to help generate bar graphs. (/view source
    <p5-graph-defs.tcl.txt>/)
tcl/p5-gei-defs.tcl
    Tcl procedures to support GEI grid pages. (/view source
    <p5-gei-defs.tcl.txt>/)
sql/cg.sql
    Common CardioGenomics Oracle tables (e.g., cg_genes). (/view source
    <cg.sql.txt>/)
sql/cg-funcs.sql
    PL/SQL functions to support database queries (e.g., cg_chrom_order)
    (/view source <cg-funcs.sql.txt>/)
sql/p5-assoc.sql
    Oracle tables specific to PGA Grid (Project 5). (/view source
    <p5-assoc.sql.txt>/)
sql/p5-funcs.sql
    PL/SQL functions to support PGA Grid queries. (/view source
    <p5-funcs.sql.txt>/)
p5.css
    Cascading Style Sheet for PGA Grid pages. (/view source <p5.css.txt>/)
p5.js
    Javascript functions for PGA Grid pages. (/view source <p5.js.txt>/)
one-snp-hw.tcl </projects/p5/hw/one-snp-hw.tcl?snp_id=86>
    Displays Hardy-Weinberg Equilibrium data for one SNP. (/view source
    <one-snp-hw.tcl.txt>/)
icon-test-utility.tcl </projects/p5/icon-test-utility.tcl>
    Developer's utility that creates random-value PGA Grid thumbnails in
    configurable sizes. Try it. (/view source <icon-test-utility.tcl.txt>/)

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View the CardioGenomics warranty disclaimer and copyright notice
</disclaimer>. The PGA Grid software package is distributed under the
GNU General Public License <http://www.gnu.org/copyleft/gpl.html>. It is
open source software which you are free to use and modify, as long as
any redistributions you may make are also covered by the GNU GPL.

Author: Steve DePalma, depalma@rascal.med.harvard.edu, 5-Dec-2005