Hello,
I would like to try this example in this link:
https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS
for example this line:
bed.fn <- system.file("extdata", "plinkhapmap.bed.gz",
package="SNPRelate")
I have in current directory from where I would run this function a
file named output4.bed
in order to run the above, can I just run this:
bed.fn <- system.file("output4.bed", package="SNPRelate")
what is "extdata" ? Do I need it if my output4.bed is in the directory
from where I am running this?
Also do I need to have .gz format of output4.bed?
Thanks
Ana
I tried to do this but I got this error:> bed.fn <- system.file("output4.bed", package="SNPRelate") > dim(bed.fn)NULL> fam.fn <- system.file("output4.fam", package="SNPRelate") > bim.fn <- system.file("output4.bim", package="SNPRelate") > snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, "HapMap.gds")Start file conversion from PLINK BED to SNP GDS ... Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE, : can only read from a binary connection In addition: Warning message: In file(filename, "rb") : file("") only supports open = "w+" and open = "w+b": using the former On Fri, Apr 10, 2020 at 2:46 PM Ana Marija <sokovic.anamarija at gmail.com> wrote:> > Hello, > > I would like to try this example in this link: > https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS > > for example this line: > > bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate") > > I have in current directory from where I would run this function a > file named output4.bed > > in order to run the above, can I just run this: > bed.fn <- system.file("output4.bed", package="SNPRelate") > > what is "extdata" ? Do I need it if my output4.bed is in the directory > from where I am running this? > > Also do I need to have .gz format of output4.bed? > > Thanks > Ana
On 10/04/2020 3:46 p.m., Ana Marija wrote:> Hello, > > I would like to try this example in this link: > https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS > > for example this line: > > bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate") > > I have in current directory from where I would run this function a > file named output4.bedJust use "output4.bed" as the filename. The system.file() function is for working out the filename of files installed in packages. Duncan Murdoch> > in order to run the above, can I just run this: > bed.fn <- system.file("output4.bed", package="SNPRelate") > > what is "extdata" ? Do I need it if my output4.bed is in the directory > from where I am running this? > > Also do I need to have .gz format of output4.bed? > > Thanks > Ana > > ______________________________________________ > R-help at 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. >
Got it, thanks! On Fri, Apr 10, 2020 at 2:54 PM Duncan Murdoch <murdoch.duncan at gmail.com> wrote:> > On 10/04/2020 3:46 p.m., Ana Marija wrote: > > Hello, > > > > I would like to try this example in this link: > > https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS > > > > for example this line: > > > > bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate") > > > > I have in current directory from where I would run this function a > > file named output4.bed > > Just use "output4.bed" as the filename. The system.file() function is > for working out the filename of files installed in packages. > > Duncan Murdoch > > > > > in order to run the above, can I just run this: > > bed.fn <- system.file("output4.bed", package="SNPRelate") > > > > what is "extdata" ? Do I need it if my output4.bed is in the directory > > from where I am running this? > > > > Also do I need to have .gz format of output4.bed? > > > > Thanks > > Ana > > > > ______________________________________________ > > R-help at 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. > > >
Hello, Could you please help unsubscribe me from these emails. Thank you. Kind Regards, Anand K Menon Cell: 1-416-939-3671 On Fri, Apr 10, 2020 at 3:46 PM Ana Marija <sokovic.anamarija at gmail.com> wrote:> Hello, > > I would like to try this example in this link: > > https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS > > for example this line: > > bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate") > > I have in current directory from where I would run this function a > file named output4.bed > > in order to run the above, can I just run this: > bed.fn <- system.file("output4.bed", package="SNPRelate") > > what is "extdata" ? Do I need it if my output4.bed is in the directory > from where I am running this? > > Also do I need to have .gz format of output4.bed? > > Thanks > Ana > > ______________________________________________ > R-help at 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. >[[alternative HTML version deleted]]
Hello, There are instructions to unsubscribe at the bottom of this e-mail and of every R-Help e-mail, see the all capital letters word. Hope this helps, Rui Barradas ?s 04:33 de 11/04/20, Anand Menon escreveu:> Hello, Could you please help unsubscribe me from these emails. Thank you. > > Kind Regards, > Anand K Menon > Cell: 1-416-939-3671 > > > On Fri, Apr 10, 2020 at 3:46 PM Ana Marija <sokovic.anamarija at gmail.com> > wrote: > >> Hello, >> >> I would like to try this example in this link: >> >> https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS >> >> for example this line: >> >> bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate") >> >> I have in current directory from where I would run this function a >> file named output4.bed >> >> in order to run the above, can I just run this: >> bed.fn <- system.file("output4.bed", package="SNPRelate") >> >> what is "extdata" ? Do I need it if my output4.bed is in the directory >> from where I am running this? >> >> Also do I need to have .gz format of output4.bed? >> >> Thanks >> Ana >> >> ______________________________________________ >> R-help at 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. >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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. >
Only you have the power to solve your problem. Follow the instructions in the footer of any R-help email. On April 10, 2020 8:33:41 PM PDT, Anand Menon <anandmenon.12 at gmail.com> wrote:>Hello, Could you please help unsubscribe me from these emails. Thank >you. > >Kind Regards, >Anand K Menon >Cell: 1-416-939-3671 > > >On Fri, Apr 10, 2020 at 3:46 PM Ana Marija ><sokovic.anamarija at gmail.com> >wrote: > >> Hello, >> >> I would like to try this example in this link: >> >> >https://www.rdocumentation.org/packages/SNPRelate/versions/1.6.4/topics/snpgdsBED2GDS >> >> for example this line: >> >> bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", >package="SNPRelate") >> >> I have in current directory from where I would run this function a >> file named output4.bed >> >> in order to run the above, can I just run this: >> bed.fn <- system.file("output4.bed", package="SNPRelate") >> >> what is "extdata" ? Do I need it if my output4.bed is in the >directory >> from where I am running this? >> >> Also do I need to have .gz format of output4.bed? >> >> Thanks >> Ana >> >> ______________________________________________ >> R-help at 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. >> > > [[alternative HTML version deleted]] > >______________________________________________ >R-help at 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.-- Sent from my phone. Please excuse my brevity.