Displaying 20 results from an estimated 1000 matches similar to: "How to obtain restricted estimates from coxph()?"
2012 Jan 18
2
Table Intersection
I've got two tables....
first one(table1):
ID chrom start end
Ex1 2 152 180
Ex2 10 2000 2220
Ex3 15 3000 4000
second one ( table2):
chrom location name
2 160 Alv
2 190 GNN
2 100
2012 Nov 05
2
fusion of overlapping intervals
Hello,
I have start and end coordinates from different experiments (DNase
hypersensitivity data) and now I would like to combine overlapping
intervals. For instance (see my test data below) (2) 30-52 and (3) 49-101
are combined to 30-101. But 49-101 and 70-103 would not be combined because
they are on different chromosomes (chr a and chr b).
Does anybody have an idea?
Thanks
Hermann
> df
2016 Apr 05
2
Is that an efficient way to find the overlapped , upstream and downstream ranges for a bunch of ranges
I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges
A range(gene) can be seem as an observation has three columns chromosome, start and end, like that
seqnames start end width strand
gene1 chr1 1 5 5 +
gene2 chr1 10 15 6 +
gene3 chr1 12 17 6 +
gene4 chr1 20 25 6 +
gene5
2011 Oct 05
6
reporting multiple objects out of a function
Dear folks,
I?m trying to build a function to create and make available some variables I
frequently use for testing purposes. Suppose I have a function that takes
some inputs and creates (internally) several named objects. Say,
fun1 <- function(x, y, z) {obj1 <- x; obj2 <- y; obj3 <- z
<missing stuff>
}
Here is the challenge: After I run it, I want the objects to be
2011 Aug 28
2
converting matrix in array
Hi everyone,
have a small problem trying to converting a dataset in matrix form to an
array.
Specifically: data include 3D measurement -x,y,z of 59 points in 36 objects.
They are stored as a matrix (x) of 2124 rows and 3 columns.
What I want to do is to extract each subject's dataset using an array (b).
Accordingly, I tried the following command:
b<-array(a,c(59,3,36)).
The problem is
2005 Jan 11
5
global objects not overwritten within function
Dear useRs,
I have a function that creates several global objects with
assign("obj",obj,.GlobalEnv), and which I need to run iteratively in
another function. The code is similar to
f <- function(...) {
assign("obj",obj,.GlobalEnv)
}
fct <- function(...) {
for (i in 1:1000)
{
...
f(...)
...obj...
rm(obj) #code fails without this line
}
}
I don't understand
2006 Jul 07
3
attach and detach question
I have a large R program that I am constantly running over and over again. At the beginning of this program, I create a hige matrix and a huge dataframe but these are constant. What I mean by constant is that, if I run the program over later, I really should just use the old matrix and dataframe ( if they exist ) that were created in a previous run so that the program doesn't have to spend
2004 Jan 16
2
reference to objects
Hi,
is there a way to reference to a data object without copying it?
For example I have a huge matrix called dist and I want two objects
obj1 and obj2 to have a memeber dist that points to the matrix, but
I don't want, for memory reasons, to copy the matrix twice.
As far as I understand the following code will generate three copies
of my data:
dist <- some_code_that_generates_data
1998 May 13
1
all.equal
I need the function all.equal which is in Splus but not yet in R. Below is a
first cut. Comments would be appreciated.
Paul Gilbert
_______
all.equal <- function(obj1, obj2, ...)
{if(mode(obj1) != mode(obj2) ) return("modes differ.")
if(class(obj1) != class(obj2)) return("classes differ.")
if(! all(unlist(attributes(obj1)) ==
2010 May 26
1
problem with not in in subseting dataframe
Hi all,
I have a problem while subsetting a dataframe that is
while I am using *%in%* condition like
*stemp<-subset(temp, obj1 %in% obj2,select=c(temp))*
this is working and giving results that what ever is there is both *obj1*and
*obj2*
**
**
but I want to get values which is there in *obj1* but not in *obj2 *
can anyone help me how to get those values.
i tried with *%o%* but i am not
2001 Oct 01
1
generic default values
I have a generic function
test.equal <- function(obj1, obj2, ...) UseMethod("test.equal")
however, the only argument that specific methods use is "fuzz" so I
would like to change this to
test.equal <- function(obj1, obj2, fuzz=???) UseMethod("test.equal")
The problem is that some methods use slightly different default values
for fuzz than others. How should
2001 Apr 09
4
fastest R platform
Hello, everyone! I picked up R several months ago and have adopted it
as my choice for statistical programming. Coming from a Java
background, I can honestly say that R is not only free, it is better
tha S-plus: the lexical scope in R makes it very simple to simulate
Java's object model. For this, I encourage everyone to read the artcle:
Robert Gentleman and Ross Ihaka (2000) "Lexical
2008 Dec 23
1
.C and 'temporaries'
Hello,
Before I get into troubles I ask here:
I make a call to a C function using .C. What I would like to know is if
the arguments in the .C call can also be 'temporary' objects.
An example will illustrate this:
# here we don't have a temporary
Obj1 = 5
.C("Func", as.integer(Obj1 ), ...) # certainly works
# here we do have a temporary
Obj2 = 5
.C("Func",
2010 Mar 14
3
likelihood ratio test between glmer and glm
I am currently running a generalized linear mixed effect model using glmer and I want to estimate how much of the variance is explained by my random factor.
summary(glmer(cbind(female,male)~date+(1|dam),family=binomial,data= liz3"))
Generalized linear mixed model fit by the Laplace approximation
Formula: cbind(female, male) ~ date + (1 | dam)
Data: liz3
AIC BIC logLik deviance
241.3
2011 Sep 07
1
access objects
hi,
say I have consecutively numbered objects obj1, obj2, ... in my R workspace.
I want to acces one of them inside a function, with the number given as an argument.
Where can I find help on how to do that? Somebody must have been trying to do this before...
Some keywords to start a search are appreciated as well.
Here's an example, I hope it clarifies what I'm trying to do:
obj1 <-
2011 Apr 15
3
DESCRIPTION file and Rd examples
I have a confusing error from R CMD check that I don't get when running the example manually by hand.
In the \examples section of an Rd file, I create a GRanges object, then I call a function with the GRanges object, whose first 2 lines are
require(GenomicRanges)
annoDF <- as.data.frame(anno) # anno is the GRanges object.
and that second line gives:
Error in
2013 Sep 06
1
directives to explicitely exclude objects from import into namespaces
Hi,
recently R CMD check --as-cran has noticed some more issues with
package namespace imports with the recommended remedy to
use importFrom() and friends.
In my case, there was only a conflict restricted to some few imports,
while I would prefer to still import all the non-conflicting objects,
methods, and classes of the respective package namespace.
So would it be possible to have some new
2005 Jul 04
3
How difficult is it to wrap a large C++ library with R?
Dear list,
I have developed a forward-time population genetics simulation
environment simuPOP, which is a set of C++ (template)
classes/functions wrapped by SWIG as Python libraries. R is used
extensively as plotting and statistical analysis engine through RPy
package.
I use Python to wrap simuPOP since most the following can be easily
done using SWIG or Python C API. However, since Python is
2005 May 07
1
Test on mu with multivariate normal distribution
Dear WizaRds,
I am sorry to bother you with a newbie question, but although I tried to solve my problem using the various .pdf files (Introduction, help pages etc.), I have come to a complete stop. Please be so kind as to guide me a little bit along my way of exploring multivariate analysis in R.
I want to test wether the means-vector mu1 of X, consisting of the means per column of that matrix
2018 Feb 26
2
lld: order of object files to be put into executable
Hi all!
Is it possible somehow to specify *order* of object files to be put to executable file?
For example, I want to put obj1.o and obj2.o somewhere at the beginning, so when executable file would be mapped
to memory, this code would be accessed quickly.