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<div class="moz-cite-prefix">Thanks you Lennart<br>
<br>
So, I guess 80 lines should be a limit for PGC.Rd.<br>
<br>
Two suggestions to the document: <br>
1) I would add a recommendation to leave comments to the C/R code.
Sometimes it is just impossible to understand what is some code
for.<br>
2) Add description at the head of to each file with code like.<br>
<br>
For example, in every file with code I ever wrote I have a small
description on the top like: <br>
<pre wrap="">//#=====================================================================================
//#
//# Filename: gtps_container.h
//#
//# Description: Set of functions for merging two snp.data class objects.
//#
//# Version: 1.0
//# Created: 18-March-2008
//# Revision: none
//#
//#
//# Author: Maksim V. Struchalin, Yurii S. Aulchenko
//# Company: ErasmusMC, Epidemiology & Biostatistics Department, The Netherlands.
//# Email: <a class="moz-txt-link-abbreviated" href="mailto:m.struchalin@@erasmusmc.nl">m.struchalin@@erasmusmc.nl</a>, <a class="moz-txt-link-abbreviated" href="mailto:i.aoultchenko@erasmusmc.nl">i.aoultchenko@erasmusmc.nl</a>
//#
//#=====================================================================================
</pre>
from which it is clear who wrote the file (person's name and
contacts), when and for whom. This is convinient for other
developers who is gonna edit this file in the future to address
their quiestions directly to the person who wrote the original
code.<br>
<br>
best,<br>
Maksim<br>
<br>
<br>
On 29/11/2013 16:25, L.C. Karssen wrote:<br>
</div>
<blockquote cite="mid:52985DA5.80400@karssen.org" type="cite">
<pre wrap="">Dear Maksim, Yakov, others,
About coding style, please see the document on GenABEL coding standards
(work in progress) we created some time ago:
<a class="moz-txt-link-freetext" href="http://genabel.r-forge.r-project.org/codingstyle.html">http://genabel.r-forge.r-project.org/codingstyle.html</a>
It would be great to have uniform coding in all of the GenABEL suite.
By the way, suggestions for additions/corrections of the document are
welcome!
Lennart.
On 11/29/2013 10:20 AM, Maksim Struchalin wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Yakov,
I made this change because when I run "R CMD check --as-cran ", I got a
message:
______________________________________________
* checking Rd line widths ... NOTE
Rd file
‘/home/maksim/work/GenABEL_project/genabel/pkg/GenABEL.Rcheck/00_pkg_src/GenABEL/man/PGC.Rd’:
\examples lines wider than 100 characters:
#result=PGC(data=chi2.1df,method="group_regress",p=freq,df=1, pol.d=2,
plot=TRUE, start.corr=FALSE,n_quiantile=3)
______________________________________________
Here are guidlines how to write .Rd files
(<a class="moz-txt-link-freetext" href="http://developer.r-project.org/Rds.html">http://developer.r-project.org/Rds.html</a>).
If I were you, I would replace "result=PGC(d..." by "result<-PGC(d..."
because using <- instead of = is common R rule for assignments.
It recommends to keep the line length in .Rd file not more then 65
characters but I guess this an old rule and now the limit is 100
characters.
best,
Maksim
On 28/11/2013 16:38, Yury Aulchenko wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Yakov,
please pay attention to this commit (I know that you were changing the
code of the GC procedures recently)
YA
On Nov 28, 2013, at 05:38 AM, <a class="moz-txt-link-abbreviated" href="mailto:noreply@r-forge.r-project.org">noreply@r-forge.r-project.org</a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Author: maksim
Date: 2013-11-28 05:38:54 +0100 (Thu, 28 Nov 2013)
New Revision: 1429
Modified:
pkg/GenABEL/man/PGC.Rd
Log:
Deleteted comments because R CMD check --as-cran said that these
lines are wider than 100 characters and they will be truncated in the
PDF manual. This should not have any influence on the code generated
from it.
Modified: pkg/GenABEL/man/PGC.Rd
===================================================================
--- pkg/GenABEL/man/PGC.Rd 2013-11-28 04:21:29 UTC (rev 1428)
+++ pkg/GenABEL/man/PGC.Rd 2013-11-28 04:38:54 UTC (rev 1429)
@@ -63,8 +63,6 @@
s <- summary(ge03d2)
freq <- s$Q.2
result=PGC(data=chi2.1df,method="median",p=freq,df=1, pol.d=2,
plot=TRUE, lmax=1.1,start.corr=FALSE)
-#"group_regress" is better to use when we have more than 50K SNPs
-#result=PGC(data=chi2.1df,method="group_regress",p=freq,df=1,
pol.d=2, plot=TRUE, start.corr=FALSE,n_quiantile=3)
}
\author{
Yakov Tsepilov
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