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

[Ana Marija]

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