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by lckarssen
Mon Jan 11, 2016 8:33 pm
Forum: GenABEL
Topic: How to convert affymetrix genotypes to GenAbel ?
Replies: 5
Views: 1650

Re: How to convert affymetrix genotypes to GenAbel ?

The fix seems easy indeed. Can you try the following updated function? "convert.snp.affymetrix" <- function(dir, map, outfile, skipaffym) { if (!is(dir, "character")) { stop("Wrong data class: the first argument should be character") } if (!is(map, "character"...
by lckarssen
Mon Jan 11, 2016 8:24 pm
Forum: GenABEL
Topic: How to convert affymetrix genotypes to GenAbel ?
Replies: 5
Views: 1650

Re: How to convert affymetrix genotypes to GenAbel ?

You're right, there seems to be no need to use ls here (line 44 of the function). R's internal file listing function should do just as well.

I've created a bug report in our bug tracker at: https://r-forge.r-project.org/tracker/i ... &atid=2058
by lckarssen
Mon Jan 11, 2016 3:42 pm
Forum: GenABEL
Topic: How to convert affymetrix genotypes to GenAbel ?
Replies: 5
Views: 1650

Re: How to convert affymetrix genotypes to GenAbel ?

Are you by any chance running this on a Windows machine?

From a quick look at the error message, it seems that the function is looking for the Unix/Linux command ls.
by lckarssen
Wed Dec 02, 2015 4:51 pm
Forum: GenABEL
Topic: [SOLVED]Egscore/gwaa.data.class not loaded properly.
Replies: 3
Views: 1790

Re: Egscore/gwaa.data.class not loaded properly.

Hi, Step 2: Load the data as a gwaa.data object: load.gwaa.data(phenofile = "pheno.dat",genofile="youroutput.dat") (...) Problem 1: Step 2 printed a lot to screen, for example: (...) and ran and finished with no complaints. So I assumed the data had been read as a gwaa class. Yo...
by lckarssen
Wed Dec 02, 2015 4:41 pm
Forum: GenABEL
Topic: [SOLVED]Having a problem with convert.snp.ped
Replies: 3
Views: 1912

Re: Having a problem with convert.snp.ped

Glad to see you have found your way around the issue.
by lckarssen
Wed Dec 02, 2015 8:52 am
Forum: GenABEL
Topic: [SOLVED]Having a problem with convert.snp.ped
Replies: 3
Views: 1912

Re: Having a problem with convert.snp.ped

Strange! Can you use /home/your_username/Genotype.map instead of using the ~? Maybe there is some problem expanding path names.
And you are sure about the capital letter G in the file name?
by lckarssen
Sat Nov 21, 2015 9:04 pm
Forum: ProbABEL
Topic: pacoxph
Replies: 5
Views: 2359

Re: pacoxph

Ah, I think I overlooked something, I must have been sleeping. I n your first post, you wrote that you were in the directory ~/ProbABEL/bin/ and then you ran palinear . But as the which command showed, you already have palinear and palogist installed in /usr/local/bin/ . I should have noticed this, ...
by lckarssen
Tue Nov 17, 2015 10:57 am
Forum: ProbABEL
Topic: pacoxph
Replies: 5
Views: 2359

Re: pacoxph

Would you give any more advices or suggestions? Do you think it would be resolved if I re-install ProbABEL? That may indeed be a good idea. Trying it won't hurt in any case. It would be great if you could then post the screen output of the make install command so we can try to track what went wrong...
by lckarssen
Mon Nov 16, 2015 9:41 am
Forum: ProbABEL
Topic: pacoxph
Replies: 5
Views: 2359

Re: pacoxph

That's strange! I just double checked and if I simply run ./configure make make install the pacoxph binary gets installed properly. Can you run the following grep command in the ProbABEL source directory? In my case it shows that building of pacoxph is enabled. Maybe it's somehow different in your c...
by lckarssen
Tue Nov 03, 2015 11:04 am
Forum: GenABEL
Topic: OmicABEL large output file issues
Replies: 4
Views: 1819

Re: OmicABEL large output file issues

Alternatively, since GenABEL is moving to github, maybe you can fork the project OmicABEL and try yourself. I would be very happy to follow your contributions and give support :) See https://github.com/GenABEL-Project/OmicABEL for the new location of OmicABEL development. As Diego said, we'd be hap...

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