[R] cannot open file '--no-restore.matrix'

[Ana Marija]

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

Please advise,
Ana

On Sat, Nov 23, 2019 at 4:16 AM Ben Tupper <btupper using 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.anamarija using 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 <btupper using 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.anamarija using 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 using 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.
> > >
> > >
> > >
> > > --
> > > 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