Search found 321 matches

by lckarssen
Wed Feb 15, 2017 11:04 am
Forum: ProbABEL
Topic: p values extracted from pacoxph output
Replies: 1
Views: 2462

Re: p values extracted from pacoxph output

Currently, the ProbABEL output only lists the chi^2 value (calculated via the likelihood ratio test) in the last column of the output. We are planning to add p-value support to the output as well , and work is on the way , but since I don't have direct funding for ProbABEL development anymore, this ...
by lckarssen
Thu Feb 09, 2017 8:42 pm
Forum: GenABEL
Topic: [SOLVED] mach2databel - Error in dimnames..
Replies: 1
Views: 2581

Re: mach2databel - Error in dimnames..

Thanks for joining the forum. I will try and see if I can reproduce this. I happen to have to convert some imputed data in VCF format to DatABEL files myself. I will get back to you in a couple of days.
by lckarssen
Fri Jan 20, 2017 8:54 am
Forum: GenABEL
Topic: Large pedigree data
Replies: 3
Views: 738

Re: Large pedigree data

Have you tried the kinship2 package? Not sure whether it has limitations in the nr. of samples.
by lckarssen
Thu Jan 19, 2017 5:17 pm
Forum: GenABEL
Topic: Large pedigree data
Replies: 3
Views: 738

Re: Large pedigree data

I don't think anybody ever used GenABEL with that many subjects. Maybe it works, maybe it won't. Do I understand correctly that you don't have genetic data, only pedigree information? It has been a while since I used GenABEL for family data, but I seem to remember it only uses genetic data to determ...
by lckarssen
Wed Jan 11, 2017 11:09 am
Forum: GenABEL
Topic: Map file questions/problems convert.snp.ped [SOLVED]
Replies: 4
Views: 1107

Re: Map file questions/problems convert.snp.ped [SOLVED]

Glad to hear the problem is solved!
by lckarssen
Sun Jan 08, 2017 10:36 pm
Forum: GenABEL
Topic: convert.snp.illumina
Replies: 1
Views: 533

Re: convert.snp.illumina

Did you be any chance create the file on Windows and use it on Linux, or the other way around? This could be the result of the different ways Linux and Windows encode the "end-of-line" character. If you created the file on Windows and now run on Linux, please use the 'dos2unix' tool to con...
by lckarssen
Tue Dec 13, 2016 8:26 am
Forum: GenABEL
Topic: SNP data for polyploids
Replies: 3
Views: 759

Re: SNP data for polyploids

I think it would be possible with some modifications. Of course. With modifications it would work. However, given that this goes down to the level of the data model, it won't be "some" modifications. It will be quite some work because many (all?) functions in the GenABEL package would nee...
by lckarssen
Mon Dec 12, 2016 11:21 am
Forum: GenABEL
Topic: Map file questions/problems convert.snp.ped [SOLVED]
Replies: 4
Views: 1107

Re: Map file questions/problems convert.snp.ped

Glad to hear you kept looking into this issue (even without bioinformatics training). I appreciate it a lot if people show willingness to dive into a problem and look/try/experiment a bit further, instead of just saying: "it doesn't work, tell me what I should type to fix it". :D Update: I...
by lckarssen
Tue Dec 06, 2016 10:39 pm
Forum: ProbABEL
Topic: palinear with mmscore - high memory use
Replies: 6
Views: 1326

Re: palinear with mmscore - high memory use

Thanks to Maarten ( see the Github issue ) I now know how I missed the memory leaks in the v0.5.0 release (the Jenkins build checks had silently failed after an upgrade). In the mean time I also fixed the issue. Do you have time to test the latest commit in the Git master branch? Or, if you haven't ...
by lckarssen
Fri Nov 25, 2016 11:24 am
Forum: GenABEL
Topic: Error in dim(rdta)
Replies: 3
Views: 707

Re: Error in dim(rdta)

hmm, those numbers shouldn't be problematic. How did you create the .raw file?

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