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by lckarssen
Thu Nov 24, 2016 8:38 am
Forum: GenABEL
Topic: convert.ped- illegal genotype (three alleles)
Replies: 5
Views: 1148

Re: convert.ped- illegal genotype (three alleles)

About the number of lines: did you create the .ped file in Linux and now use GenABEL on Windows or the other way around?

How many lines do you expect in the .ped file? 200 (i.e. 200 samples)?
by lckarssen
Thu Nov 24, 2016 8:36 am
Forum: GenABEL
Topic: convert.ped- illegal genotype (three alleles)
Replies: 5
Views: 1148

Re: convert.ped- illegal genotype (three alleles)

dahgam72 wrote:The file is not tped file.


I'm a bit confused: the title of the topic mentions convert.ped, the code that you pasted says convert.tped. So, your data is in .ped format. Just to be sure, which function did you use?
by lckarssen
Wed Nov 23, 2016 12:02 pm
Forum: GenABEL
Topic: SNP data for polyploids
Replies: 3
Views: 935

Re: SNP data for polyploids

As far as I know, GenABEL was developed with human genomes in mind. I would have to double check, but I'm quite sure there is no option for polyploids.
by lckarssen
Wed Nov 23, 2016 12:00 pm
Forum: GenABEL
Topic: Error in dim(rdta)
Replies: 3
Views: 838

Re: Error in dim(rdta)

How many SNPs and IDs should there be in this data set?
by lckarssen
Wed Nov 23, 2016 11:59 am
Forum: GenABEL
Topic: convert.ped- illegal genotype (three alleles)
Replies: 5
Views: 1148

Re: convert.ped- illegal genotype (three alleles)

As the error message says: it seems that you have a triallelic SNP in line 201. Have you verified that line in the tped file?
by lckarssen
Tue Nov 22, 2016 9:03 am
Forum: ProbABEL
Topic: palinear with mmscore - high memory use
Replies: 6
Views: 1475

Re: palinear with mmscore - high memory use

Wow... 10× more RAM usage is definitely not good.

I have opened issue #31 on Github to track this issue.
by lckarssen
Wed Nov 16, 2016 1:41 pm
Forum: ProbABEL
Topic: palinear with mmscore - high memory use
Replies: 6
Views: 1475

Re: palinear with mmscore - high memory use

Good idea to run a simulated phenotype. Looking forward to the outcome!
by lckarssen
Wed Nov 16, 2016 8:52 am
Forum: ProbABEL
Topic: palinear with mmscore - high memory use
Replies: 6
Views: 1475

Re: palinear with mmscore - high memory use

That's interesting... As you already supposed, this kind of memory consumption is not expected. 6000 individuals and 5M SNPs should work. Given that you only have phenotype data on 800 of them might (or might not) point to the problematic part of the code. In my personal experience we usually had ph...
by lckarssen
Fri Aug 26, 2016 7:21 am
Forum: ProbABEL
Topic: Publications using ProbAbel
Replies: 1
Views: 953

Re: Publications using ProbAbel

I don't have list like that lying around, but you could check out the papers that cite the original ProbABEL paper from 2009: https://scholar.google.nl/scholar?cites=4765499743273161221&as_sdt=2005&sciodt=0,5&hl=nl Similarly, a Google Scholar search of "ProbABEL GWAS -probable"...
by lckarssen
Wed Aug 03, 2016 10:06 am
Forum: ProbABEL
Topic: Regression analysis on a subset of IDs
Replies: 2
Views: 1092

Re: Regression analysis on a subset of IDs

The --nids option is a bit weird. I never really understood its use. When the option is set (e.g. to a number n ), only the first n individuals will be used. So, apart from only using the first n individuals there is no way to select a subset of individuals. I have added this as an issue in our bug ...

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