Hi all,
First, I carried out GO enrichment to predicted/validated target genes of those
miRNA using GOstats package. Then I find myself in a dead end. So what is the
good practice? Is it possible to directly do GO enrichment to miRNAs? Are they
included in GO database?
Regards,
Allen
[[a
Hello,
I use getSymbols function daily to run some models with stock data. Today
when I tried to update the stock info i get this error
Error in charToDate(x) :
character string is not in a standard unambiguous format
Sometimes I get it after 2 symbols, other times after 150 symbols, another
t
#How to add a legend for this bubble plot
#I prefer p2 with a legend for each bubble
library(graphics)
set.seed(1234)
n=20
x <- rnorm(n)*2
y <- rnorm(n) * 1/10
Z <- rnorm(n)+ 100
df$r <- sqrt(z/pi)
df$l <- replicate(n, paste(sample(LETTERS, 3, replace=TRUE), collapse=""))
N <- nrow(df)
I have sought consultation online and in person, to no avail. I hope someone
on here might have some insight. Any feedback would be most welcome.
I am attempting to plot predicted values from a two-component hurdle model
(logistic [suicide attempt yes/no] and negative binomial count [number of
att
If you use the lubridate package, this is very easy.
See the help file for month() within lubridate for more examples.
library(lubridate)
x <- now()
month(x)
month(x, label = TRUE)
month(x, label = TRUE, abbr = FALSE)
as.character(month(x, label = TRUE, abbr = FALSE))
When you run the above your
Don't the functions metaMDSdist() and metaMDSredist() that are documented on
the metaMDS manual page give you the distance matrix? If you want to compute
the distances based on a single axis, you could use vegdist().
David C
-Original Message-
From: r-help-boun...@r-project.org [mailto
Dear R users,
I would like to access the distance matrix generated by metaMDS as well as
use the dist function to calculate the euclidean distance for each axis in
the NMDS. I am having trouble finding a way to access these variables and
any help is greatly appreciated.
For the distance matrix I
For future reference, perhaps creating an index variable when the data
frame is first created and before ³multiple process and ordering² is done
would be good.
mydat$index <- seq(nrow(mydat))
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925
Hi,
I would like to deploy a R script such that it can be run as batch commando
on generic Window machines.
After reading a bit about deploy possibilities I see that the recommended
way is to include the whole R installation catalog and then run R from
command line from within that catalog.
Howev
While there are tools that claim to compute power for tests beyond
what you find in the pwr package, I don't like to use them because
either I don't agree with the assumptions that they make, or I don't
know what assumptions are being made (and therefore I don't know
whether I agree with them or no
Yihui,
Thank you so much. I read the PANDOC.md as you suggested and this solved my
issue. I've created the soft-links and then I run in linux terminal
$ echo "rmarkdown::render('teste01.Rmd')" | R --vanilla
R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for S
On 07/30/2014 05:00 AM, r-help-requ...@r-project.org wrote:
A while ago, I inquired about fitting excess relative risk models in R. This is
a follow-up about what I ended up doing in case the question pops up again.
While I was not successful in using standard tools, switching to Bayesian
mo
On Aug 28, 2014, at 12:29 PM, varin sacha wrote:
> Dear all,
>
> I do know very well the pwr packages from Stéphane Champely.
> I would have known if somebody knows others packages for power analysis ?
The Hmisc/rms package combo has some power oriented functions and I have a
vague memory th
I have a set of data with ~ 250,000 observations summarized in ~ 1000 rows that
I'm trying to analyze with mlogit. Based on the discussion in
https://stat.ethz.ch/pipermail/r-help/2010-June/241161.html
I understand that using weights= does not (fully) do what I need. I tried
expanding my data t
Dear all,
I do know very well the pwr packages from St�phane Champely.�
I would have known if somebody knows others packages for power analysis ?�
I think here more about the calculation of the power analysis of the
nonparametric tests like the mann whitney or the kruskall wallis.
Best Regards,
Please check out the instructions here:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Creating an alias might work, although I have not really tried. What I
have been doing is to uninstall the old version of Pandoc in my
system, and create symlinks following the instructions above. Yo
Hello,
I want to render a Rmd file using rmarkdown::render() function but I'm used
to edit files with Emacs and I open a linux terminal session to compile
this file with knitr::knit2html()
## On the linux terminal.
$ echo "require(knitr); knit2html('teste01.Rmd')" | R --vanilla
I want to use rma
Delete all characters up to and including the last hyphen with
sub(".*-", "", test)
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Thu, Aug 28, 2014 at 10:41 AM, Jun Shen wrote:
> Hi everyone,
>
> I believe I am not the first one to have this problem but couldn't find a
> relevant thread o
Thanks for everyone who replied with those wonderful solutions!
Jun
On Thu, Aug 28, 2014 at 2:11 PM, Enrico Schumann
wrote:
> On Thu, 28 Aug 2014, Jun Shen writes:
>
> > Hi everyone,
> >
> > I believe I am not the first one to have this problem but couldn't find a
> > relevant thread on the l
On Thu, 28 Aug 2014, Jun Shen writes:
> Hi everyone,
>
> I believe I am not the first one to have this problem but couldn't find a
> relevant thread on the list.
>
> Say I have a string (actually it is the whole column in a data frame) in a
> format like this:
>
> test<- 'AF14-485-502-89-00235'
>
On Aug 28, 2014, at 12:41 PM, Jun Shen wrote:
> Hi everyone,
>
> I believe I am not the first one to have this problem but couldn't find a
> relevant thread on the list.
>
> Say I have a string (actually it is the whole column in a data frame) in a
> format like this:
>
> test<- 'AF14-485-502
Here's one way:
R> test<- 'AF14-485-502-89-00235'
R> test2 <- strsplit(test, "-")
R> test2
[[1]]
[1] "AF14" "485" "502" "89""00235"
R> test2[[1]][length(test2[[1]])]
[1] "00235"
On Thu, Aug 28, 2014 at 1:41 PM, Jun Shen wrote:
> Hi everyone,
>
> I believe I am not the first one to have
Hi everyone,
I believe I am not the first one to have this problem but couldn't find a
relevant thread on the list.
Say I have a string (actually it is the whole column in a data frame) in a
format like this:
test<- 'AF14-485-502-89-00235'
I would like to split the test string and keep the last
R users,
Abstracts are now being accepted for electronic poster presentations at the
2015 ASA Conference on Statistical Practice, February 19-21, New Orleans,
Louisiana, USA.
If you are interested, you may submit your abstract on the website,
http://www.amstat.org/meetings/csp/2015/abstracts.cfm
On Thu, Aug 28, 2014 at 11:45 AM, Martin Spindler
wrote:
> Dear all,
> I would like to us openBLAS in R under Linux / Unix.
> Which steps do I have to undertake? Does someone know a detailed
> description? (I found some sources on the web, but none was really
> helpful for me.)
> Thanks and best,
Such problems usually come from not understanding where files really are,
though sometimes odd file permissions can be the culprit. Understanding how
backslashes work in R strings also sometimes causes problems, though you seem
to be using forward slashes so that may not apply here.
You may fin
You didn't give your results (but DID give a script -- hooray!). I made
a small change -- got rid of the bounds and added trace=TRUE, and got
the output
## after 5001Jacobian and 6997 function evaluations
## namecoeff SE tstat pval
gradientJSingval
#
At 16:38 27/08/2014, Owen, Branwen wrote:
Thank you very much for your quick reply Wolfgang. The 0 does make
sense - I'm working on some behavioural data and in one study none
reported that particular behaviour. Up til now I have been
calculating I2 without that study, as it's on the small side
Hi,
You don't show us your code, and you really should, but most likely
you did not put the file where you thought you did, or there's a typo
in the name.
Using file.choose() may help.
Also, I think it's bad practice to put user files in the R library
directory. You should make a working directo
Put it into a SQL database, MySQL or PostgreSQL.
el
on 2014-08-28, 00:01 Grant Rettke said the following:
> Good evening,
>
> Suppose that /the business/ want to store tabular data inside of a
> file. They want manage that file using a GUI program that runs on OSX,
> Linux, and Windows. Additio
Dear R Group,
I have an species occurence file stored in dismo/ex/abc.csv.
When i read the file, it shows error.
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") : cannot open file
'G:/Software/R-3.1.1/library/dismo/ex/occurence.csv': No suc
Dear all,
I would like to us openBLAS in R under Linux / Unix.
Which steps do I have to undertake? Does someone know a detailed
description? (I found some sources on the web, but none was really
helpful for me.)
Thanks and best,
Martin
[[alternative HTML version deleted]]
__
Try:
format(as.Date("05/07/2014", "%m/%d/%Y"), "%m")
#[1] "05"
#or
strptime("05/07/2014", "%m/%d/%Y")$mon+1
#[1] 5
A.K.
How to extract a Month from Date object?
almost 13 peoples visited my Question with out replying in New to R , i have
task yaar
don't mind plz could you HELP ME
How t
Hello,
If your data.frame is named 'dat', try something like the following.
dat[order(rownames(dat)), ]
Hope this helps,
Rui Barradas
Em 28-08-2014 08:56, Ragia Ibrahim escreveu:
Dear all,
I have a data frame, where multible process and ordering done ..can I re
arrange (re order ) it rega
Dear all,
I have a data frame, where multible process and ordering done ..can I re
arrange (re order ) it regarding it' s original ROW index ? how?
example
Xi items numrber_list_items
38 8, 7, 3, 44
27 7, 3, 40
1 10 10
Thank you Martin for your advices.
Let me give more information about my matrices. I am working on a
space-time model, it is a very simple model based on second-moment
assumption. My model is
E(Y) = g(X%*%beta) -> g is a suitable link function
V(Y) = C = V^{1/2} Omega V^{1/2} -> It is my variance
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