[R] How to access values in s4 method
Hi How to access the values in the output that is an object of S4 type. I tried to access using subset ( [ ] ) but it is not allowed. Any clue?? Thanks -- Fahim #My code is as follows: require(IRanges); query <- IRanges(c(1, 4, 9), c(5, 7, 10)) subject <- IRanges(c(2, 2, 10), c(2, 3, 12)) findOverlaps(query, subject) Output of find overlap function is: -- 1> findOverlaps(query, tree) An object of class "RangesMatching" Slot "matchMatrix": query subject [1,] 1 1 [2,] 1 2 [3,] 3 2 Slot "DIM": [1] 4 3 How to access the values in the output? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] union data in column
Is there any function/way to merge/unite the following data GENEID col1 col2 col3col4 G234064 1 0 0 0 G234064 1 0 0 0 G234064 1 0 0 0 G234064 0 1 0 0 G234065 0 1 0 0 G234065 0 1 0 0 G234065 0 1 0 0 G234065 0 0 1 0 G234065 0 0 1 0 G234065 0 0 0 1 into GENEID col1 col2 col3col4 G234064 1 1 0 0 // 1 appears in col1 and col2 above, rest are zero G234065 0 1 1 1 // 1 appears in col2 , 3 and 4 above. Thanks -- Fahim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] calling a c function from R
Thanks a lot Matt,
Just if someone like to see how I called a C function from R with files as
argumets.
For simplicity, this example is copying the content of input file into
output file
-
My main program is :
source("parse.R")
parseGBest('gbest40.seq', 'gbest40.out'); // .seq is input file, .out is
output file
---
I wrote a wrapper function (parse.R) as follows:
dyn.load("parse.so");
parseGBest= function(infile, outfile)
{
# Do some whatever you like here
.C("parse", infile, outfile)
}
--
parse.c File looks like follows:
#include
#include
#include
#include
void adel(char **infile, char **outfile)
{
char line[81];
FILE *fr, *of;
if (!(fr = fopen(*infile, "r")))
{
fprintf(stdout, "Error while opening input file\n");
return ;
}
if (!(of = fopen(*outfile, "w")))
{
fprintf(stdout, "Error while opening output file\n");
return ;
}
while(fgets(line, 81, fr) != NULL)
{
fputs(line, of);
}
fclose(fr);
fclose(of);
}
--
Thats it!
I saved almost a week in parsing all those genbank est files(almost 413
files).
Thanks R&C interface team.
--Fahim
On Wed, Jul 14, 2010 at 10:18 AM, Matt Shotwell wrote:
> Fahim,
>
> Please see the Writing R Extensions manual
> http://cran.r-project.org/doc/manuals/R-exts.pdf
>
> There are simple instructions in this document under the heading "System
> and foreign language interfaces."
>
> -Matt
>
>
> On Wed, 2010-07-14 at 01:21 -0400, Fahim Md wrote:
> > Hi,
> > I am trying to call a C function, that I wrote to parse a flat file,
> into
> > R. The argument that will go into this function is an input file that I
> need
> > to parse and write the desired output in an output file. I used some hit
> > and trial approach but i keep on getting the "file not found" or
> > "segmentation fault" error. I know that the error is in passing the
> argument
> > but I could not solve it.
> >
> > After reading some of the tutorials, I understood how to do this if the
> > arguments are integers or floats. I am stuck when i am trying to send the
> > files. I am attaching stub of each file.
> > Help appreciated.
> > Thanks
> >
> > ---
> > My function call would be:
> > source("parse.R")
> > parseGBest('./gbest/inFile.seq', './gbest/outFile.out');
> > ---
> > I wrote a wrapper function (parse.R) as follows:
> >
> > dyn.load("parse.so");
> > parseGBest = function(inFile, outFile)
> > {
> > .C( "parse" , inFile , outFile);
> > }
> >
> > How to write receive the filenames in function( , ) above. and how to
> call
> > .C
> >
> >
> > parse.c file is as below: How to receive the argument in funcion and how
> to
> > make it compatible with my argv[ ].
> >
> >
> > void parse( int argc, char *argv[] ) //This is working as standalone C
> > program. How to receive
> > // the above files so
> that
> > it become compatible with my argv[ ]
> > {
> >
> > FILE *fr, *of;
> > char line[81];
> >
> >
> > if ( *argc == 3 )*/
> > {
> > if ( ( fr = fopen( argv[0], "r" )) == NULL )
> > {
> > puts( "Can't open input file.\n" );
> > exit( 0 );
> > }
> > if ( ( of = fopen( argv[1], "w" )) == NULL )
> > {
> > puts( "Output file not given.\n" );
> > }
> > }
> >else
> > {printf("wrong usage: Try Agay!!! correct usage is:=
> functionName
> > inputfileToParse outFileToWriteInto\n");
> >}
> > while(fgets(line, 81, fr) != NULL)
> >
> > --
> > ---
> > --
> > }
> >
> >
> >
> > Thanks again
> > Fahim
> >
> --
> Matthew S. Shotwell
> Graduate Student
> Division of Biostatistics and Epidemiology
> Medical University of South Carolina
> http://biostatmatt.com
>
>
--
Fahim Mohammad
Bioinforformatics Lab
University of Louisville
Louisville, KY, USA
Ph: +1-502-409-1167
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and provide commented, minimal, self-contained, reproducible code.
[R] calling a c function from R
Hi,
I am trying to call a C function, that I wrote to parse a flat file, into
R. The argument that will go into this function is an input file that I need
to parse and write the desired output in an output file. I used some hit
and trial approach but i keep on getting the "file not found" or
"segmentation fault" error. I know that the error is in passing the argument
but I could not solve it.
After reading some of the tutorials, I understood how to do this if the
arguments are integers or floats. I am stuck when i am trying to send the
files. I am attaching stub of each file.
Help appreciated.
Thanks
---
My function call would be:
source("parse.R")
parseGBest('./gbest/inFile.seq', './gbest/outFile.out');
---
I wrote a wrapper function (parse.R) as follows:
dyn.load("parse.so");
parseGBest = function(inFile, outFile)
{
.C( "parse" , inFile , outFile);
}
How to write receive the filenames in function( , ) above. and how to call
.C
parse.c file is as below: How to receive the argument in funcion and how to
make it compatible with my argv[ ].
void parse( int argc, char *argv[] ) //This is working as standalone C
program. How to receive
// the above files so that
it become compatible with my argv[ ]
{
FILE *fr, *of;
char line[81];
if ( *argc == 3 )*/
{
if ( ( fr = fopen( argv[0], "r" )) == NULL )
{
puts( "Can't open input file.\n" );
exit( 0 );
}
if ( ( of = fopen( argv[1], "w" )) == NULL )
{
puts( "Output file not given.\n" );
}
}
else
{printf("wrong usage: Try Agay!!! correct usage is:= functionName
inputfileToParse outFileToWriteInto\n");
}
while(fgets(line, 81, fr) != NULL)
--
---
--
}
Thanks again
Fahim
--
Fahim Mohammad
Bioinforformatics Lab
University of Louisville
Louisville, KY, USA
Ph: +1-502-409-1167
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and provide commented, minimal, self-contained, reproducible code.
[R] Is there any function to read genbank flat files.
Hi I am trying to read genbank est flat files. Is there any function in R to do that. I was looking for something similar to SeqIO.parse(input_handle, "genbank") in bioPython that convert the genebank sequence into fasta sequence. (One option is to call biopython from R but I am not familiar with python functions so I want to avoid that and I am keeping it as last resort) Thanks and regards. --Fahim -- Fahim Mohammad Bioinforformatics Lab University of Louisville Louisville, KY, USA Ph: +1-502-409-1167 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] installing a package in linux
I recently started using ubuntu 9.10 and I am using gedit editor and R
plugin for writing R code. To install any package I need to do:
$ install.packages()
//window pop-up for mirror selection
//then another window pop up for package selection.
After this as long as I am not exiting, the function of the newly installed
packages are available.
After I exit (i use to put 'no' in 'save workspace' option) from R, if I
want to again work in R, I have to repeat the process of package install.
This reintallation problem was not there in windows(I was using Tinn-R as
editor, I just need to put require('package-name') to use its function).
Is there anyway so that reinstallation of the package is avoided???
thanks
--Fahim
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and provide commented, minimal, self-contained, reproducible code.
[R] using BLAT in r
Does anyone know how to use BLAT(Blast-Like alignment tool) in R? Thanks and regards. -- Fahim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] variable three dimensional array
I am using R for my bioinformatics research. I am dealing with a graph in
which I need to find all possible path. I was looking for some package that
solve my purpose
but all in vain. There are available algorithms but most of them find
shortest path that ignore other paths So I decided to write my own from
scratch.
I need to create a two dimensional matrix of size nXn.
The element of each entry may contain (node,edge) pair in the form of
bit-vector.
eg. (mat is the matrix)
mat[1,1] = NULL
mat[1,2] = {1, 1100} #first entry is node vector and second
entry is edge vector
mat[1,3] = {{01000, 01001000}, {00100, 0110}} #Here there are two
node-edge pair. There can be more also, so it is variable.
In other sense it can be said that, the matrix is a 3-d matrix with a
variable third dimension.
I tried the problem with list but I was partially succesful.
Any suggestion in this regard will be highly appreciated.
thanks
---Fahim
Louisville, KY, USA
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[R] problem with paste function
Hi there!!
I am having trouble with *paste* function. I dont know how to proceed. I
tried many options but i failed miserably.
I am using a variable f1 to assign a string as below:
f1=dataLine[locAffyProbeID];
( the value of f1 is *244901_at* )
Then I am using the paste function
paste("set g=", f1);
instead of getting *set g=244901_at*, I am getting *set g=23*.
I am not able to understand why it is so.
Can anyone help!!!Please..
Thanks
--
Mohammad Fahim
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and provide commented, minimal, self-contained, reproducible code.
[R] PRoblem with paste function
Hi there!!!
I am having trouble with *paste* function. I dont know how to proceed. I
tried many options but i failed miserably.
I am using a variable f1 to assign a string as below:
f1=dataLine[locAffyProbeID];
( the value of f1 is *244901_at* )
Then I am using the paste function
paste("set @g1=", f1);
instead of getting *...@g1=244901_at*, I am getting *set @g1=23*.
I am not able to understand why it is so.
Can anyone help!!!Please..
Thanks
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
