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 ______________________________________________ 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.
