Hi Eric,Thanks for the explanation. Is there a way to save the results
automatically after the analysis gets over?. As I recently lost the results,
because I didn't save the results. I don't want to run the sink or save
command after the analysis is over rather run the command for saving the file
before starting to run the analysis, so the file gets saved automatically after
the script has finished running
Priya
?
On Wednesday, 1 November 2017 7:53 PM, Eric Berger <ericjberger at
gmail.com> wrote:
Hi Priya,
You did not follow the logic of the pseudo-code.?The sink("filename"),
sink() pair captures whatever output is generated between the first sink
statement and the second sink statement.You need (possibly) to do:
sink("C://Users//Priya// Desktop//Attractor analysis_all
genes//synaptogenesis//attr. txt")
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_
signaling_submodule3.txt")attr <- getAttractors(net,
type="asynchronous")
sink()
HTH,Eric
?
On Wed, Nov 1, 2017 at 4:10 PM, Priya Arasu <galaxie2485 at yahoo.co.in>
wrote:
Hi Eric,I tried as you suggested but I could not find the output in the text
file I created (attr.txt)
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_
signaling_submodule3.txt")sink("C://Users//Priya// Desktop//Attractor
analysis_all genes//synaptogenesis//attr. txt")
sink()
attr <- getAttractors(net, type="asynchronous")
?Priya
On Wednesday, 1 November 2017 6:54 PM, Eric Berger <ericjberger at
gmail.com> wrote:
Some comments:1. sink() does not return a value. There is on point to set attr
<- sink(...). Just give the command sink("C://....etc")2. to
complete the saving to the file you must give a second sink command with no
argument:? sink()So your code would be (pseudo-code, not actual code)
sink( "filename" )do something that prints output which will be
captured by sinksink()
HTH,Eric
On Wed, Nov 1, 2017 at 1:32 PM, Priya Arasu via R-help <r-help at
r-project.org> wrote:
Hi,I want the results to be saved automatically in a output text file after the
script has finished running.
I used the sink function in the following example, but the results file
(output.txt) was empty.
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_ signaling_submodule3.txt")#
First I loaded theinput file for which I want to identify attractors
attr <- sink("C://Users//Priya// Desktop//Attractor analysis_all
genes//synaptogenesis//output. txt")# used the sink function to save the
results from attr function
attr <- getAttractors(net, type="asynchronous")# then ran the
script for identifying attractors
Is there any function to save the results before setting the script to run, so
that results are automatically saved in a text file after the script has
finished running?
Thank youPriya
? ? ? ? [[alternative HTML version deleted]]
______________________________ ________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
[[alternative HTML version deleted]]
Let's try a simple example.> # Create a script file of commands > # Note we must print the results of quantile explicitly > cat("x <- rnorm(50)\nprint(quantile(x))\nstem(x)\n", file="Test.R") > > # Test it by running it to the console > source("Test.R")0% 25% 50% 75% 100% -2.4736219 -0.7915433 -0.1178056 0.7023577 2.9158617 The decimal point is at the | -2 | 510 -1 | 7631110 -0 | 9988777333333211 0 | 01124455557777889 1 | 00045 2 | 19> > # Now run it and save the file > sink("Testout.txt") > source("Test.R") > sink() > > # What is located in "Testout.txt"? > cat(readLines("Testout.txt"), sep="\n")0% 25% 50% 75% 100% -2.47511893 -0.47919111 0.05761628 0.67403447 1.79825459 The decimal point is at the | -2 | 5 -2 | 4 -1 | -1 | 432000 -0 | 87755 -0 | 4433332110 0 | 001244 0 | 55666667777789 1 | 113 1 | 5788> # SuccessDepending on your operating system, you may also be able to save the output with File | Save to File. --------------------------------------- David L Carlson Department of Anthropology Texas A&M University College Station, TX 77843-4352 -----Original Message----- From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Priya Arasu via R-help Sent: Wednesday, November 1, 2017 9:57 AM To: Eric Berger <ericjberger at gmail.com> Cc: r-help at r-project.org Subject: Re: [R] Function to save results Hi Eric,Thanks for the explanation. Is there a way to save the results automatically after the analysis gets over?. As I recently lost the results, because I didn't save the results. I don't want to run the sink or save command after the analysis is over rather run the command for saving the file before starting to run the analysis, so the file gets saved automatically after the script has finished running Priya ? On Wednesday, 1 November 2017 7:53 PM, Eric Berger <ericjberger at gmail.com> wrote: Hi Priya, You did not follow the logic of the pseudo-code.?The sink("filename"), sink() pair captures whatever output is generated between the first sink statement and the second sink statement.You need (possibly) to do: sink("C://Users//Priya// Desktop//Attractor analysis_all genes//synaptogenesis//attr. txt") net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all genes//synaptogenesis// regulationof_dopamine_ signaling_submodule3.txt")attr <- getAttractors(net, type="asynchronous") sink() HTH,Eric ? On Wed, Nov 1, 2017 at 4:10 PM, Priya Arasu <galaxie2485 at yahoo.co.in> wrote: Hi Eric,I tried as you suggested but I could not find the output in the text file I created (attr.txt) net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all genes//synaptogenesis// regulationof_dopamine_ signaling_submodule3.txt")sink("C://Users//Priya// Desktop//Attractor analysis_all genes//synaptogenesis//attr. txt") sink() attr <- getAttractors(net, type="asynchronous") ?Priya On Wednesday, 1 November 2017 6:54 PM, Eric Berger <ericjberger at gmail.com> wrote: Some comments:1. sink() does not return a value. There is on point to set attr <- sink(...). Just give the command sink("C://....etc")2. to complete the saving to the file you must give a second sink command with no argument:? sink()So your code would be (pseudo-code, not actual code) sink( "filename" )do something that prints output which will be captured by sinksink() HTH,Eric On Wed, Nov 1, 2017 at 1:32 PM, Priya Arasu via R-help <r-help at r-project.org> wrote: Hi,I want the results to be saved automatically in a output text file after the script has finished running. I used the sink function in the following example, but the results file (output.txt) was empty. net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all genes//synaptogenesis// regulationof_dopamine_ signaling_submodule3.txt")# First I loaded theinput file for which I want to identify attractors attr <- sink("C://Users//Priya// Desktop//Attractor analysis_all genes//synaptogenesis//output. txt")# used the sink function to save the results from attr function attr <- getAttractors(net, type="asynchronous")# then ran the script for identifying attractors Is there any function to save the results before setting the script to run, so that results are automatically saved in a text file after the script has finished running? Thank youPriya ? ? ? ? [[alternative HTML version deleted]] ______________________________ ________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Hi David,Thank you for the example.When I try to use the cat function, I get an
error
cat(attr<-getAttractors(net, type="asynchronous"))Error in cat(attr
<- getAttractors(net, type = "asynchronous")) :
argument 1 (type 'pairlist') cannot be handled by 'cat'
Please let me know, if I have used the function in right way?.
Thank you
Priya
?
On Wednesday, 1 November 2017 9:32 PM, David L Carlson <dcarlson at
tamu.edu> wrote:
Let's try a simple example.
> # Create a script file of commands
> # Note we must print the results of quantile explicitly
> cat("x <- rnorm(50)\nprint(quantile(x))\nstem(x)\n",
file="Test.R")
>
> # Test it by running it to the console
> source("Test.R")
? ? ? ? 0%? ? ? ? 25%? ? ? ? 50%? ? ? ? 75%? ? ? 100%
-2.4736219 -0.7915433 -0.1178056? 0.7023577? 2.9158617
? The decimal point is at the |
? -2 | 510
? -1 | 7631110
? -0 | 9988777333333211
? 0 | 01124455557777889
? 1 | 00045
? 2 | 19
>
> # Now run it and save the file
> sink("Testout.txt")
> source("Test.R")
> sink()
>
> # What is located in "Testout.txt"?
> cat(readLines("Testout.txt"), sep="\n")
? ? ? ? 0%? ? ? ? 25%? ? ? ? 50%? ? ? ? 75%? ? ? ? 100%
-2.47511893 -0.47919111? 0.05761628? 0.67403447? 1.79825459
? The decimal point is at the |
? -2 | 5
? -2 | 4
? -1 |
? -1 | 432000
? -0 | 87755
? -0 | 4433332110
? 0 | 001244
? 0 | 55666667777789
? 1 | 113
? 1 | 5788
> # Success
Depending on your operating system, you may also be able to save the output with
File | Save to File.
---------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352
-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Priya Arasu
via R-help
Sent: Wednesday, November 1, 2017 9:57 AM
To: Eric Berger <ericjberger at gmail.com>
Cc: r-help at r-project.org
Subject: Re: [R] Function to save results
Hi Eric,Thanks for the explanation. Is there a way to save the results
automatically after the analysis gets over?. As I recently lost the results,
because I didn't save the results. I don't want to run the sink or save
command after the analysis is over rather run the command for saving the file
before starting to run the analysis, so the file gets saved automatically after
the script has finished running Priya
?
? ? On Wednesday, 1 November 2017 7:53 PM, Eric Berger <ericjberger at
gmail.com> wrote:
Hi Priya,
You did not follow the logic of the pseudo-code.?The sink("filename"),
sink() pair captures whatever output is generated between the first sink
statement and the second sink statement.You need (possibly) to do:
sink("C://Users//Priya// Desktop//Attractor analysis_all
genes//synaptogenesis//attr. txt") net <-
loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_
signaling_submodule3.txt")attr <- getAttractors(net,
type="asynchronous")
sink()
HTH,Eric
?
Hi Eric,I tried as you suggested but I could not find the output in the text
file I created (attr.txt)
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_
signaling_submodule3.txt")sink("C://Users//Priya// Desktop//Attractor
analysis_all genes//synaptogenesis//attr. txt")
sink()
attr <- getAttractors(net, type="asynchronous")
?Priya
? ? On Wednesday, 1 November 2017 6:54 PM, Eric Berger <ericjberger at
gmail.com> wrote:
Some comments:1. sink() does not return a value. There is on point to set attr
<- sink(...). Just give the command sink("C://....etc")2. to
complete the saving to the file you must give a second sink command with no
argument:? sink()So your code would be (pseudo-code, not actual code) sink(
"filename" )do something that prints output which will be captured by
sinksink() HTH,Eric
On Wed, Nov 1, 2017 at 1:32 PM, Priya Arasu via R-help <r-help at
r-project.org> wrote:
Hi,I want the results to be saved automatically in a output text file after the
script has finished running.
I used the sink function in the following example, but the results file
(output.txt) was empty.
net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor analysis_all
genes//synaptogenesis// regulationof_dopamine_ signaling_submodule3.txt")#
First I loaded theinput file for which I want to identify attractors attr <-
sink("C://Users//Priya// Desktop//Attractor analysis_all
genes//synaptogenesis//output. txt")# used the sink function to save the
results from attr function
attr <- getAttractors(net, type="asynchronous")# then ran the
script for identifying attractors Is there any function to save the results
before setting the script to run, so that results are automatically saved in a
text file after the script has finished running?
Thank youPriya
? ? ? ? [[alternative HTML version deleted]]
______________________________ ________________ R-help at r-project.org mailing
list -- To UNSUBSCRIBE and more, see 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.
?
?
??? [[alternative HTML version deleted]]
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.
[[alternative HTML version deleted]]
Hi Priya,
I think your original question may have been phrased in a way that caused
David and me some confusion.
I think sink() may not be the function that is appropriate in your case.
Sink() is used to capture output to the console (so to speak).
You are trying to save the results of calculations returned, in this case
in the variable 'attr'.
You need to do something like:
attr <- getAttractors( ... )
saveRDS( attr, "filename.RDS")
and then later you can read the results back in another R session:
savedAttr <- readRDS("filename.RDS")
Look at the documentation ?saveRDS and ?readRDS
HTH,
Eric
On Wed, Nov 1, 2017 at 6:02 PM, David L Carlson <dcarlson at tamu.edu>
wrote:
> Let's try a simple example.
>
> > # Create a script file of commands
> > # Note we must print the results of quantile explicitly
> > cat("x <- rnorm(50)\nprint(quantile(x))\nstem(x)\n",
file="Test.R")
> >
> > # Test it by running it to the console
> > source("Test.R")
> 0% 25% 50% 75% 100%
> -2.4736219 -0.7915433 -0.1178056 0.7023577 2.9158617
>
> The decimal point is at the |
>
> -2 | 510
> -1 | 7631110
> -0 | 9988777333333211
> 0 | 01124455557777889
> 1 | 00045
> 2 | 19
>
> >
> > # Now run it and save the file
> > sink("Testout.txt")
> > source("Test.R")
> > sink()
> >
> > # What is located in "Testout.txt"?
> > cat(readLines("Testout.txt"), sep="\n")
> 0% 25% 50% 75% 100%
> -2.47511893 -0.47919111 0.05761628 0.67403447 1.79825459
>
> The decimal point is at the |
>
> -2 | 5
> -2 | 4
> -1 |
> -1 | 432000
> -0 | 87755
> -0 | 4433332110
> 0 | 001244
> 0 | 55666667777789
> 1 | 113
> 1 | 5788
>
> > # Success
>
> Depending on your operating system, you may also be able to save the
> output with File | Save to File.
>
> ---------------------------------------
> David L Carlson
> Department of Anthropology
> Texas A&M University
> College Station, TX 77843-4352
>
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Priya
> Arasu via R-help
> Sent: Wednesday, November 1, 2017 9:57 AM
> To: Eric Berger <ericjberger at gmail.com>
> Cc: r-help at r-project.org
> Subject: Re: [R] Function to save results
>
> Hi Eric,Thanks for the explanation. Is there a way to save the results
> automatically after the analysis gets over?. As I recently lost the
> results, because I didn't save the results. I don't want to run the
sink or
> save command after the analysis is over rather run the command for saving
> the file before starting to run the analysis, so the file gets saved
> automatically after the script has finished running Priya
>
>
>
> On Wednesday, 1 November 2017 7:53 PM, Eric Berger <
> ericjberger at gmail.com> wrote:
>
>
> Hi Priya,
> You did not follow the logic of the pseudo-code. The
sink("filename"),
> sink() pair captures whatever output is generated between the first sink
> statement and the second sink statement.You need (possibly) to do:
> sink("C://Users//Priya// Desktop//Attractor analysis_all
> genes//synaptogenesis//attr. txt") net <-
loadNetwork("C://Users//Priya/
> /Desktop//Attractor analysis_all genes//synaptogenesis//
> regulationof_dopamine_ signaling_submodule3.txt")attr <-
getAttractors(net,
> type="asynchronous")
> sink()
> HTH,Eric
>
>
>
> On Wed, Nov 1, 2017 at 4:10 PM, Priya Arasu <galaxie2485 at
yahoo.co.in>
> wrote:
>
> Hi Eric,I tried as you suggested but I could not find the output in the
> text file I created (attr.txt)
>
> net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor
analysis_all
> genes//synaptogenesis// regulationof_dopamine_
signaling_submodule3.txt")sink("C://Users//Priya//
> Desktop//Attractor analysis_all genes//synaptogenesis//attr. txt")
>
>
> sink()
>
> attr <- getAttractors(net, type="asynchronous")
> Priya
>
>
> On Wednesday, 1 November 2017 6:54 PM, Eric Berger <
> ericjberger at gmail.com> wrote:
>
>
> Some comments:1. sink() does not return a value. There is on point to set
> attr <- sink(...). Just give the command sink("C://....etc")2.
to complete
> the saving to the file you must give a second sink command with no
> argument: sink()So your code would be (pseudo-code, not actual code) sink(
> "filename" )do something that prints output which will be
captured by
> sinksink() HTH,Eric
>
>
> On Wed, Nov 1, 2017 at 1:32 PM, Priya Arasu via R-help <
> r-help at r-project.org> wrote:
>
> Hi,I want the results to be saved automatically in a output text file
> after the script has finished running.
>
> I used the sink function in the following example, but the results file
> (output.txt) was empty.
>
> net <- loadNetwork("C://Users//Priya/ /Desktop//Attractor
analysis_all
> genes//synaptogenesis// regulationof_dopamine_
signaling_submodule3.txt")#
> First I loaded theinput file for which I want to identify attractors attr
> <- sink("C://Users//Priya// Desktop//Attractor analysis_all
> genes//synaptogenesis//output. txt")# used the sink function to save
the
> results from attr function
>
> attr <- getAttractors(net, type="asynchronous")# then ran the
script for
> identifying attractors Is there any function to save the results before
> setting the script to run, so that results are automatically saved in a
> text file after the script has finished running?
>
> Thank youPriya
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________ ________________ R-help at r-project.org
> mailing list -- To UNSUBSCRIBE and more, see 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.
>
>
>
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>
[[alternative HTML version deleted]]