just in case someone is also running into the error 127 when using the function with system(): system() does not like spaces' ' in the directory. e.g. Test Folder. Just convert it to TestFolder and it works. Btw: kudo to your channel!
Amazing videos! Thank you! But I keep running into an error "Failed to open "filename"" when tying to run the Quality control line with either runPLINK or system functions. Do you have any idea why that might be the case?
Hi, In case of these error message one of the following is most likely: 1) You have a typo in your script or in the filename on your HDD. Ensure these are exactly the same 2) The working directory is not set correctly. If you write getwd() on your R comand line, it wil show the currect working directory. This is the place where your data should be located 3) only the base PLINK file name should be stated in the PLINK line, so "plink --file myData.ped " will result into similar error. You just need to write "plink --file myData " 4) You try to open a ped+map file using --bfile, or binary ped files using --file in PLINK. The appropriate option should be used. Did this solve your problem?
Hi, In the video, the solution works only for linking the specific folder. If you are advanced enough with R, you can create a custom package, where you could include the PLINK executable file, with a very similar effect, as described in this video. Right now, for this to work, this package with the corresponding function should be available in the R package repository CRAN. Well... Interestingly, there is a package called "plink", but it does something totally different. You can search for it here: cran.r-project.org/web/packages/available_packages_by_name.html#available-packages-P Even more interestingly, there is a package "plinkQC", which seems to be focusing on various quality control aspects of the program, and package "plinkFile" which reads and writes PLINK data files in and out of R. Both of these are quite specific. For general work they are not suitable, i.e. these packages are not designed to deliver the full functionality of the program. So it depends on what you want to do...
Sorry, no. If the executable does not run, I always try with the tutorial data, or just alone. Even if it prints a "file not found" error message, I know it works. If there are similar weird messages, it might be a compilation issue (e.g. compiled for a different operating system), or just a corrupted exe file
Profesor congratulations for you videos, so I have one question for you: To use plink with the pig organism, what is the possible command(e.g.--chr) according to your example from the video-tutorial? Thanks you!
Hi! Pigs do not have a shortcut implemented in PLINK, so the "--chr-set 18" command should be added to the line (without the quotation mark). Pigs have 18 autosomes, that is the reason for the number 18.
I can't believe this channel exist!
I can't thank you enough, you are helping my master degree!
Thank you!!
you taught us this power method. thk u. Gabor. all the best!
So interesting, I gave been patiently waiting for your new videos.
just in case someone is also running into the error 127 when using the function with system():
system() does not like spaces' ' in the directory. e.g. Test Folder. Just convert it to TestFolder and it works.
Btw: kudo to your channel!
Thanks! Yes, spaces and (language-specific) special characters could be problematic in file and folder names, so it is best to avoid them entirely.
Oh god, thank you! you're a Chad
Amazing videos! Thank you! But I keep running into an error "Failed to open "filename"" when tying to run the Quality control line with either runPLINK or system functions. Do you have any idea why that might be the case?
Hi,
In case of these error message one of the following is most likely:
1) You have a typo in your script or in the filename on your HDD. Ensure these are exactly the same
2) The working directory is not set correctly. If you write getwd() on your R comand line, it wil show the currect working directory. This is the place where your data should be located
3) only the base PLINK file name should be stated in the PLINK line, so "plink --file myData.ped " will result into similar error. You just need to write "plink --file myData "
4) You try to open a ped+map file using --bfile, or binary ped files using --file in PLINK. The appropriate option should be used.
Did this solve your problem?
Would it work if we install plink package in R then write the command in R as library(plink) ？
Hi,
In the video, the solution works only for linking the specific folder. If you are advanced enough with R, you can create a custom package, where you could include the PLINK executable file, with a very similar effect, as described in this video.
Right now, for this to work, this package with the corresponding function should be available in the R package repository CRAN. Well... Interestingly, there is a package called "plink", but it does something totally different. You can search for it here: cran.r-project.org/web/packages/available_packages_by_name.html#available-packages-P
Even more interestingly, there is a package "plinkQC", which seems to be focusing on various quality control aspects of the program, and package "plinkFile" which reads and writes PLINK data files in and out of R.
Both of these are quite specific.
For general work they are not suitable, i.e. these packages are not designed to deliver the full functionality of the program. So it depends on what you want to do...
Hi, have you ever encountered the error bad CPU in executable?
Sorry, no.
If the executable does not run, I always try with the tutorial data, or just alone. Even if it prints a "file not found" error message, I know it works.
If there are similar weird messages, it might be a compilation issue (e.g. compiled for a different operating system), or just a corrupted exe file
Profesor congratulations for you videos, so I have one question for you: To use plink with the pig organism, what is the possible command(e.g.--chr) according to your example from the video-tutorial?
Thanks you!
Hi! Pigs do not have a shortcut implemented in PLINK, so the "--chr-set 18" command should be added to the line (without the quotation mark). Pigs have 18 autosomes, that is the reason for the number 18.
@@GenomicsBootCamp Thanks for you aswer!!!
there is no scripts here