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 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 > >>>>> 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. > > > ______________________________________________ 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.