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 <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 > > > > 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 ______________________________________________ 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.