Search found 322 matches

by lckarssen
Sun Feb 28, 2016 10:30 pm
Forum: GenABEL
Topic: Convert table to gwaa-class
Replies: 1
Views: 1064

Re: Convert table to gwaa-class

I think a quicker way to plot a manhattan plot is to use the QQMan R package: http://www.gettinggeneticsdone.com/2014/05/qqman-r-package-for-qq-and-manhattan-plots-for-gwas-results.html It will save you the step of converting the data to a different object type and QQman allows easy customisation of...
by lckarssen
Sun Feb 28, 2016 10:25 pm
Forum: GenABEL
Topic: Problem with convert.snp.ped
Replies: 2
Views: 1362

Re: Problem with convert.snp.ped

We have had several reports of buggy behaviour of the convert.snp.ped function. Maybe this is another one of those. Could you try to use the convert.snp.tped function? This seems to behave better.
by lckarssen
Sun Feb 28, 2016 10:21 pm
Forum: ProbABEL
Topic: Issue with the input files for analysis
Replies: 1
Views: 2372

Re: Issue with the input files for analysis

1) Will I be able to run an analysis with the provided files? I don't seem to have a file with the phenotype of interest and the covariates. In principle you can run association analysis with the data in these VCF files, but as you noted reformatting is required since ProbABEL doesn't know how to r...
by lckarssen
Tue Feb 23, 2016 2:45 pm
Forum: ProbABEL
Topic: Palogist analysis 1100.00% done
Replies: 2
Views: 1422

Re: Palogist analysis 1100.00% done

Wow... That's interesting! :D How did you monitor the screen output of palogist? Did you submit jobs to a queue system (e.g. Sun GridEngine or PBS)? Or did you run the analyses one by one on the command line? Which version of ProbABEL did you use? If the number of lines in the output files (use wc -...
by lckarssen
Fri Feb 19, 2016 9:21 pm
Forum: GenABEL
Topic: convert.snp.illumina First three fields are missing line 2
Replies: 3
Views: 2360

Re: convert.snp.illumina First three fields are missing line 2

Hmm, interesting... Can you tell me how many rows and columns your input file has?
by lckarssen
Fri Feb 19, 2016 9:10 pm
Forum: GenABEL
Topic: convert.snp.ped argument 2 matches multiple formal arguments
Replies: 1
Views: 1625

Re: convert.snp.ped argument 2 matches multiple formal arguments

> convert.snp.ped(ped='HWWAMP_Complete.plk.ped', map="HWWAMP_Complete.plk.map", out='HWWAMP.out') Error in convert.snp.ped(ped = "HWWAMP_Complete.plk.ped", map = "HWWAMP_Complete2.plk.map", : argument 2 matches multiple formal arguments The filenames are unique within ...
by lckarssen
Fri Feb 19, 2016 9:02 pm
Forum: ProbABEL
Topic: [SOLVED] probABEL error
Replies: 3
Views: 1856

Re: probABEL error

Glad to hear you figured it out! Thanks for letting us know.
by lckarssen
Fri Feb 05, 2016 11:20 pm
Forum: ProbABEL
Topic: [SOLVED] probABEL error
Replies: 3
Views: 1856

Re: probABEL error

Hi, It looks like you already did quite a few things trying to solve the issue. Let me check a few assumptions : ⋅ you try to read from DatABEL files, right? ⋅ which version of ProbABEL do you use? Dou you by any chance know what the data is at the indicated location? You could u...
by lckarssen
Tue Jan 26, 2016 5:34 pm
Forum: GenABEL
Topic: Multiple phenotype per genotype
Replies: 2
Views: 1390

Re: Multiple phenotype per genotype

The way the tools in the GenABEL suite are structured is that sample IDs must be unique. My first idea for a work-around is to recode the place variables as 0/1 and add column for each place. This way the places will be treated as regular (binary) covariates. However, I guess that won't work in your...
by lckarssen
Thu Jan 14, 2016 1:24 pm
Forum: GenABEL
Topic: impute2mach error
Replies: 21
Views: 12735

Re: impute2mach error

That's great to hear! Thank you for confirming this. I will incorporate this fix and try to get a new version of the package out as soon as I have time.

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