Hi Duncan, thanks, I just did, Rscript --no-save MR.R ENSG00000154803.ld ENSG00000154803.matrix [1] "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 On Sat, Nov 23, 2019 at 12:13 PM Duncan Murdoch <murdoch.dun...@gmail.com> wrote: > > On 23/11/2019 11:05 a.m., Ana Marija wrote: > > 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 > > You didn't put the print(cmd_args) into the script. > > Duncan Murdoch > > > > > > 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.
