cannot open file '--no-restore.matrix'

cmd_args=commandArgs(TRUE)
print(cmd_args)

cmd_args=commandArgs()
print(cmd_args)

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 <btupper at 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.anamarija at 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 <btupper at 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 at 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

--
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