On 23/11/2019 1:21 p.m., Ana Marija wrote:
Hi Duncan,
thanks, I just did,
Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix
[1] "ENSG00000154803.ld" "ENSG00000154803.matrix"
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'NA.matrix': No such file or directory
Execution halted
Your script works with the third element in the list of arguments, and
there are only two.
Duncan Murdoch
Please advise
On Sat, Nov 23, 2019 at 12:13 PM Duncan Murdoch
<murdoch.dun...@gmail.com> wrote:
On 23/11/2019 11:05 a.m., Ana Marija wrote:
Hi Ben,
I am not sure what you mean when you say to print, is it this?
cmd_args=commandArgs(TRUE)
print(cmd_args)
character(0)
cmd_args=commandArgs()
print(cmd_args)
[1] "/software/linux-el7-x86_64/compilers/r-3.6.1/lib64/R/bin/exec/R"
I changed in the first line of this script:
https://github.com/eleporcu/TWMR/blob/master/MR.R
cmd_args=commandArgs() to be cmd_args=commandArgs(TRUE)
but again I get the same error:
Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'NA.matrix': No such file or directory
Execution halted
You didn't put the print(cmd_args) into the script.
Duncan Murdoch
Please advise,
Ana
On Sat, Nov 23, 2019 at 9:44 AM Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
On 23/11/2019 10:26 a.m., Ana Marija wrote:
HI Ben,
I tried it but it doesn't work:
Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '--no-restore.matrix': No such file or directory
Execution halted
You should print the cmd_args variable that is set on the first line of
that script. When I run a script that prints it using your command
line, this is what it looks like:
$ Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix
[1] "/Library/Frameworks/R.framework/Resources/bin/exec/R"
[2] "--slave"
[3] "--no-restore"
[4] "--no-save"
[5] "--file=MR.R"
[6] "--args"
[7] "ENSG00000154803.ld"
[8] "ENSG00000154803.matrix"
The next line
gene <- cmd_args[3]
is obviously wrong for my system, because it would set gene to
"--no-restore". Your results will probably be somewhat different, but
it might be clear what you should use instead of the third element.
By the way, changing the first line
cmd_args=commandArgs()
to
cmd_args <- commandArgs(TRUE)
makes a lot of sense in most cases. I haven't read your whole script so
I don't know it it makes sense for you.
Duncan Murdoch
Please advise,
Ana
On Sat, Nov 23, 2019 at 4:16 AM Ben Tupper <btup...@bigelow.org> wrote:
Hi,
I think you want this order...
Rscript [options for R] script_file.R argument_1 argument_2 ...
So, like this ...
Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix
Cheers,
Ben
On Fri, Nov 22, 2019 at 8:59 PM Ana Marija <sokovic.anamar...@gmail.com> wrote:
HI Ben,
thank you so much , I did this:
Rscript --no-save ENSG00000154803.ld ENSG00000154803.matrix MR.R
Error: unexpected numeric constant in "1.000 0.089"
Execution halted
I made ENSG00000154803.ld with:
library(MASS)
write.matrix(ENSG00000154803.ld, file="ENSG00000154803.ld")
and it looks like this:
1.000 0.089 0.006 0.038 0.012 0.014 0.003 0.001 0.005 0.015 0.013
0.000 0.000 0.000 0.001 0.003 0.000
0.089 1.000 0.002 0.007 0.005 0.001 0.004 0.005 0.000 0.003 0.014
0.001 0.012 0.005 0.000 0.004 0.004
0.006 0.002 1.000 0.004 0.008 0.029 0.040 0.001 0.001 0.006 0.013
0.054 0.006 0.002 0.010 0.001 0.000
0.038 0.007 0.004 1.000 0.460 0.044 0.008 0.022 0.010 0.229 0.095
0.066 0.010 0.030 0.001 0.003 0.000
0.012 0.005 0.008 0.460 1.000 0.151 0.018 0.047 0.021 0.272 0.185
0.002 0.003 0.066 0.006 0.004 0.004
0.014 0.001 0.029 0.044 0.151 1.000 0.007 0.018 0.218 0.010 0.023
0.016 0.000 0.025 0.000 0.005 0.000
0.003 0.004 0.040 0.008 0.018 0.007 1.000 0.003 0.002 0.020 0.031
0.128 0.019 0.005 0.030 0.002 0.016
0.001 0.005 0.001 0.022 0.047 0.018 0.003 1.000 0.004 0.014 0.004
0.098 0.010 0.012 0.001 0.006 0.003
0.005 0.000 0.001 0.010 0.021 0.218 0.002 0.004 1.000 0.004 0.000
0.012 0.000 0.006 0.018 0.004 0.013
0.015 0.003 0.006 0.229 0.272 0.010 0.020 0.014 0.004 1.000 0.466
0.001 0.091 0.057 0.062 0.002 0.005
0.013 0.014 0.013 0.095 0.185 0.023 0.031 0.004 0.000 0.466 1.000
0.238 0.180 0.073 0.058 0.000 0.006
0.000 0.001 0.054 0.066 0.002 0.016 0.128 0.098 0.012 0.001 0.238
1.000 0.158 0.006 0.044 0.006 0.001
0.000 0.012 0.006 0.010 0.003 0.000 0.019 0.010 0.000 0.091 0.180
0.158 1.000 0.077 0.237 0.009 0.000
0.000 0.005 0.002 0.030 0.066 0.025 0.005 0.012 0.006 0.057 0.073
0.006 0.077 1.000 0.056 0.000 0.004
0.001 0.000 0.010 0.001 0.006 0.000 0.030 0.001 0.018 0.062 0.058
0.044 0.237 0.056 1.000 0.000 0.003
0.003 0.004 0.001 0.003 0.004 0.005 0.002 0.006 0.004 0.002 0.000
0.006 0.009 0.000 0.000 1.000 0.002
0.000 0.004 0.000 0.000 0.004 0.000 0.016 0.003 0.013 0.005 0.006
0.001 0.000 0.004 0.003 0.002 1.000
the other file (ENSG00000154803.matrix) looks like this:
GENES ENSG00000154803 BETA_GWAS
rs12601631 -0.320577 -0.0160778
rs1708623 0.708706 0.0717719
rs1708628 -0.645996 -0.0973019
rs17804843 -0.78984 0.0059607
rs4078062 -0.340732 -0.0716837
rs4316813 -0.721137 -0.00502219
rs7217764 -0.61641 0.16997
rs7221842 -0.377727 -0.00184011
rs12602831 -0.397059 0.0154625
rs138437542 -0.590669 0.0145733
rs2174369 -0.167913 -0.0268728
rs242252 0.20184 0.0161709
rs34121330 0.328602 0.0753894
rs4792798 -0.303601 0.00227314
rs7222311 -0.367686 -0.0419168
rs74369938 0.687555 -0.223105
rs8075751 -0.261916 -0.0313484
On Fri, Nov 22, 2019 at 7:44 PM Ben Tupper <btup...@bigelow.org> wrote:
Hi,
You might check the order of your arguments. Options come before the
script filename. See the details here...
https://www.rdocumentation.org/packages/utils/versions/3.6.1/topics/Rscript
Ben
On Fri, Nov 22, 2019 at 8:17 PM Ana Marija <sokovic.anamar...@gmail.com> wrote:
Hello,
I am trying to run this code:
https://github.com/eleporcu/TWMR/blob/master/MR.R
with r-3.6.1
via:
Rscript MR.R --no-save ENSG00000154803
in the current directory I have saved: ENSG00000154803.ld and
ENSG00000154803.matrix as the software requires
but I am getting this error:
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '--no-restore.matrix': No such file or directory
Execution halted
Please advise,
Thanks
Ana
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Ben Tupper
Bigelow Laboratory for Ocean Science
West Boothbay Harbor, Maine
http://www.bigelow.org/
https://eco.bigelow.org
--
Ben Tupper
Bigelow Laboratory for Ocean Science
West Boothbay Harbor, Maine
http://www.bigelow.org/
https://eco.bigelow.org
______________________________________________
R-help@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.
______________________________________________
R-help@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.
