WetlandOpenwater
[21] iniBed_m maxH_m BoxID
$output_fclasses
[1] 0 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 4
$dataset_options
NULL
$layer_options
NULL
--
Scott M. Duke-Sylvester
Assistant Professor
Department of Biology
Office : 300 E. St. Mary Blvd
Billeaud Hall, Room
-1062
On 8/17/12 9:28 AM, Scott Duke-Sylvester scottdukesylves...@gmail.com
wrote:
I have a quick question: It appears that in rgdal v0.7-12 (R version
2.15.1, OSX 10.6.8) writeOGR will not write a shapefile the the
current directory. Is this correct? An earlier version of rgdal must
have
: Saturday, January 28, 2012 8:12 PM
To: Duke; r-help@r-project.org
Subject: Re: [R] percentage from density()
If you use logspline estimation (logspline package) instead of kernel density
estimation then this is
simple as there are cumulative area functions for logspline fits.
If you need to do
Hi folks,
I know that density function will give a estimated density for a give
dataset. Now from that I want to have a percentage estimation for a
certain range. For examle:
y = density(c(-20,rep(0,98),20))
plot(y, xlim=c(-4,4))
Now if I want to know the percentage of data lying in
useR's,
I am trying to do a power calculation for a survival analysis using a
logrank test and I need some help properly doing this in R. Here is the
information that I know:
- I have 2 groups, namely HG and LG
- Retrospective analysis with subjects gathered from archival data over 20
years. No
Thanks for your response, Marc. HG and LG are high-grade/low-grade tumors.
The data has not been collected yet, but will be soon. It's all archived
data that will be pulled from computer records. The IRB wants some mention
of power or sample size, but doing it for this scenario has been a bit
Hi folks,
Please let me know what I am doing wrong. I want to have a legend with
symbols that are filled with same color as the drawn line, but I failed
to do that:
plot(1:100, 1:100, pch=21, bg=red)
legend(bottomright, test, bty='n', pch=21, bg=red, col=red)
It looks to me that the bg
On 9/15/11 4:40 PM, Duke wrote:
Hi folks,
Please let me know what I am doing wrong. I want to have a legend with
symbols that are filled with same color as the drawn line, but I
failed to do that:
plot(1:100, 1:100, pch=21, bg=red)
legend(bottomright, test, bty='n', pch=21, bg=red, col=red
On 2/24/11 1:21 PM, David Winsemius wrote:
On Feb 24, 2011, at 1:03 PM, Duke wrote:
Hi folks,
I am wondering if the following is possible: I want to control the
arguments sent to a function by string variables. For example,
instead of
heatmap.2( A, col=greenred(75) )
I would want to have
Hi folks,
I am wondering if the following is possible: I want to control the
arguments sent to a function by string variables. For example, instead of
heatmap.2( A, col=greenred(75) )
I would want to have something like:
heatmap.2 ( paste(A, col=greenred(75), sep=,) )
Is this possible to do
Hi all,
I am new to heatmap function in stats package, so any advice will be
greatly appreciated. So I have a dataset that I want to draw a heatmap,
for example:
dput(a)
structure(c(-8.256023, -14.764429, -10.145779, -5.123104, -11.974729,
-16.329029, -16.329029, -16.329029, -2.764114,
On 1/12/11 6:44 PM, Duke wrote:
Thanks so much for your suggestion Martin. I had Bioconductor
installed but I honestly do not know all its applications. Anyway, I
am testing GenomicRanges with my data now. I will report back when I
get the result.
I got the results. My code took ~ 580
Sorry for the late response. I was away for vacation and was unable to
keep on working on the codes.
Anyway, I was unable to provide *str* of that specific data since they
are all in a big package with lots of inputs/outputs. Quickly gazing
through the code, I narrowed them down (and made a
Hi folks,
I am working on a project that requires subsetting of a found file based
on some known file. The known file contains several lines like below:
chr132375463237547rs523104280+
chr132375493237550rs520975820+
chr245133264513327
On 1/12/11 6:12 PM, Martin Morgan wrote:
The Bioconductor project has many tools for dealing with
sequence-related data. With the data
k - read.table(textConnection(
chr132375463237547rs523104280+
chr132375493237550rs520975820+
chr245133264513327
Hi all,
First I dont have much experience with R so be gentle. OK, I am dealing
with a dataset (~ tens of thousand lines, each line ~ 10 columns of
data). I have to create some subset of this data based on some certain
conditions (for example, same first column with another dataset etc...).
Hi Jim,
Is this really a problem for me to use [1] instead of [[1]]? Will this
make it run slower? Also, if I use dat$V1 %in% list$V1, will it be fine?
Anyway, my data and list are basically gene lists (tab delimited):
$ head test.txt
Xkr4chr1-320456236615793206102
Actually there are different ways of doing subsetting:
[1]
[[1]]
[,1]
$V1
Please let me know which one is the fastest (and most used) one. Thanks.
D.
On 12/30/10 11:28 AM, Duke wrote:
Hi Jim,
Is this really a problem for me to use [1] instead of [[1]]? Will this
make it run slower? Also
Hi all,
I am trying to plot a venn diagram using vennDiagram in limma package,
but I have no idea how to have it colorful such as the color one created
by the following website: http://www.pangloss.com/seidel/Protocols/venn.cgi.
Any one has any advice?
Thanks,
D.
Hi Laurent,
On 12/7/10 5:01 PM, Laurent Gatto wrote:
Dear Duke,
I'm not sure if limma can generate colourful Venn diagrams. As an
alternative, I can however recommend Vennerable [1].
Thanks. I also found out that there are so many packages drawing venn
diagram now. I am playing
On 9/16/10 5:00 PM, Rolf Turner wrote:
On 17/09/2010, at 8:51 AM, Duke wrote:
Hi Duncan,
On 9/16/10 3:47 PM, Duncan Murdoch wrote:
On 16/09/2010 3:40 PM, Duke wrote:
Hi all,
I am writing a function (fun.R), but I dont know how to code the
function so that the Help Text will be shown
, R or python.
Dukeduke.li...@gmx.com wrote:
On 9/16/10 5:00 PM, Rolf Turner wrote:
On 17/09/2010, at 8:51 AM, Duke wrote:
Hi Duncan,
On 9/16/10 3:47 PM, Duncan Murdoch wrote:
On 16/09/2010 3:40 PM, Duke wrote:
Hi all,
I am writing a function (fun.R), but I dont know how to code
Hi all,
I am writing a function (fun.R), but I dont know how to code the
function so that the Help Text will be shown up when one types ?fun (of
course, after he loads it up). Anyone has any advice for me how to do that?
Thanks,
D.
__
Hi Duncan,
On 9/16/10 3:47 PM, Duncan Murdoch wrote:
On 16/09/2010 3:40 PM, Duke wrote:
Hi all,
I am writing a function (fun.R), but I dont know how to code the
function so that the Help Text will be shown up when one types ?fun (of
course, after he loads it up). Anyone has any advice
Hi all,
I have to filter a tab-delimited text file like below:
GeneNamesvalue1value2log2(Fold_change)
log2(Fold_change) normalizedSignature(abs(log2(Fold_change)
normalized) 4)
ENSG0209350435-3.81131293562629-4.14357714689656TRUE
ENSG0177133
Hi Phil,
On 9/10/10 1:45 PM, Phil Spector wrote:
Duke -
One possibility is to check the help files for the functions
involved to see if there are options to control this behaviour.
For example, the check.names= argument to read.table, or the quote=
argument to write.table. How about
Yes
On 9/10/10 2:49 PM, Gabor Grothendieck wrote:
On Fri, Sep 10, 2010 at 1:24 PM, Dukeduke.li...@gmx.com wrote:
Hi all,
I have to filter a tab-delimited text file like below:
GeneNamesvalue1value2log2(Fold_change)
log2(Fold_change) normalizedSignature(abs(log2(Fold_change)
On 9/10/10 4:24 PM, Gabor Grothendieck wrote:
On Fri, Sep 10, 2010 at 4:20 PM, Dukeduke.li...@gmx.com wrote:
On 9/10/10 2:49 PM, Gabor Grothendieck wrote:
On Fri, Sep 10, 2010 at 1:24 PM, Dukeduke.li...@gmx.comwrote:
Hi all,
I have to filter a tab-delimited text file like below:
On 9/6/10 12:18 PM, Stephen Liu wrote:
Hi folks,
Debian 504 64-bit
I found following document;
http://www.biostat.wisc.edu/~kbroman/Rintro/
Whether it is the right document for installing Emacs+ESS and R so that R can
run on Emacs?
A lot on the web. Google gave me for example:
On 4/27/10 6:29 PM, mtmor...@fhcrc.org wrote:
Welcome to R!
But actually, I should be saying 'welcome to Bioconductor!' and you
should be on the Bioconductor (or Bioc-sig-seq) mailing list
http://bioconductor.org/docs/mailList.html
because ShortRead is a Bioconductor package.
BWA
On 4/27/10 8:04 PM, Duncan Murdoch wrote:
On 27/04/2010 6:15 PM, Duke wrote:
Hi all,
I am testing R by trying R on command line (ie without opening R
console) on a Mac Pro with 10.6. So I created a file plot.R:
x11(width=5,height=3.5)
plot(1:10,1:10)
So I have two questions below (please
On 4/28/10 9:53 AM, Duncan Murdoch wrote:
On 28/04/2010 9:38 AM, Duke wrote:
On 4/27/10 8:04 PM, Duncan Murdoch wrote:
On 27/04/2010 6:15 PM, Duke wrote:
Hi all,
I am testing R by trying R on command line (ie without opening R
console) on a Mac Pro with 10.6. So I created a file plot.R
On 4/28/10 10:16 AM, peter dalgaard wrote:
On Apr 28, 2010, at 4:03 PM, Duke wrote:
I just did it, and it said it ignored the arg:
$ R R_PROFILE_USER=try.R
ARGUMENT 'R_PROFILE_USER=try.R' __ignored__
...
What am I doing wrong?
Using Windows syntax on a Unix
Dear folks,
Please welcome a newbie both to R and the mailing list :). I am
currently working on a sequencing project, and heard about R as well as
some of its packages for next gen sequencing, and decided to give it a
try. Starting with ShortRead, I found a document
Hi all,
I am testing R by trying R on command line (ie without opening R
console) on a Mac Pro with 10.6. So I created a file plot.R:
x11(width=5,height=3.5)
plot(1:10,1:10)
So I have two questions below (please forgive me if the questions have
been asked already)
1. What is the different
or outside the polygons defined in the shapefile.
Many thanks,
scott.
--
Scott M. Duke-Sylvester
Assistant Professor
Department of Biology
Office : 300 E. St. Mary Blvd
Billeaud Hall, Room 141
Lafayette, LA 70504
Mailing address : UL Lafayette
Department
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