Created rawData vignette

I am trying R markdown to markdown with knitr and then markdown to html5 with pandoc.  Also note that this vignette requires package CleftCNVAssoc which is not available anywhere but enigma.
Translated inherited deletions vignette from Sweave format to R markdown format

Also updated rawData with asciidoc or pandoc... not sure.
Updated rawData vignette.
Updated rawData vignette.
Updated vignettes and included a build script for the web-site
Simple update of raw data vignettes
Updated and created more raw data vignettes
Transposed inherited deletions vignette to asciidoc with embedded figures

courtesy of karl broman
Updated inherited-deletions vignette.

Now we count as transmitted all deletions that have a transmitted component anywhere in the region.  It takes an hour to count for all approximately two thousand regions.  Tomorrow I will use binom.test to compute the CIs for the transmission rate.

Note that a trio with trio-state 111 is ambiguousm as it is both a transmission and a non-transmission.  Currently it is counted towards transmitted and not towards untransmitted.
Clean up

Here I cleaned out extraneous files and added to the .gitignore file --- all in an effort to keep things minimal.

Bumped the version --- mostly just to update the date in the DESCRIPTION file ;)
More clean up.

Here I removed files associated with the inherited deletions vignette that were needed for my earlier report generation method, i.e., R markdown and pandoc.

Also updated .gitignore to contain make.out, the hilariously named log file generated with make and Makefile.
Included asciidoc.R in repo.

asciidoc.R is a script that executes the Asciidoc() command.  The filename must be updated --- currently it is used for inherited-deletions.
Updated Inherited Deletions Vignette.

On the web page there is now a link to the New Counting method within the CLP Association vignette.  Here we implement the change in counting and plot a histogram of overall tranmission rates per region, as well as the CIs per region , stratified by cleft, control, and all.

We still see regions of undertransmission.  If our hypothesis is that these are regions with excessive false positve rates, and that they should be eliminated from the study than we need a systematic way to categorize bad regions.

It still may be worthwhile to investigate correlation between marker density and under-transmission.  Some physical property, whether it is biology, or the chip design, is likely to be causing the under-transmission/false positives.
Updated Inherited Deletions vignette.

Now, we also see in the vignette the construction of the CNV matrices and FamilyExperiment objects.

We are relying heavily on caching within Asciidoc.  Most but, not all of the R code is evaluated.  The construction of the CNV matrix and counting transmissions by region are both comutationally intensive, taking about an hour each.

Note that the vignette could not be run from start to finish from scratch.  There are two instances where th epackage would beed to be reinstalled and reloaded.  This is due to saving data in the ./data/ directory at two steps.
A few small changes to inherited deletions vignette.

Cleaned up some whitespace.

Added a line to show the number of regions that are included in analysis.Note that right now regions with one component are not being considered.  It is highly unlikely that a region with over 50 observed deltions will only have one component.  Nonetheless there are a lot of them and we need to consider them.  This will be done soon, but it was a priority to get the figures finished for Terri's progress report.
Fixed bug in new counting method.

This bug was due to the classic R error of expecting a set of indices to have length greater than one.  When there is only one index, the matrix becomes a vector and things fall apart.  It seems to be fixed, but I haven't run it yet on all of the regions.
Update to Inherited Deletions vignette.

No changes since the last commit to the source code.  These changes are just the result of re-running the vignette.  Note that this was a trial and used only the first 100 regions.  Next I need to run it on all of the two thousand some regions.
Having difficulties getting Inherited Deletions vignette running.

Not sure what the problem is here, but I think it might be caching.  Let's see how it goes on my home computer.
Re-ran entire Inherited Deletions vignette.

To be sure that all is well I ran the entire vignette without caching and all is indeed well.  I was worried about some caching issues that may have benn occurring at work.
Updated Inherited Deletions vignette.

Now, we identify the CIs for the two significant regions.  We do so in the CI figures, as well as printing out the values.