[SOLVED] probABEL palinear --mmscore function.

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manonb
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Joined: Mon Feb 07, 2011 3:47 pm

[SOLVED] probABEL palinear --mmscore function.

Postby manonb » Mon Feb 07, 2011 4:36 pm

Hello all,
First, I am very happy to join this ABEL forum! I am an extensive user of this package, so you hear will from me often... :D
To start with, I have a little question for the probABEL palinear --mmscore function:
Will I get different results for a specific snp if I supply a smaller region to palinear –mmscore containing that snp VS a larger region containing that snp?
In other words, if I divide my chromosome 3 in 5 different regions and run palinear 5 times with the different regions VS running palinear only once with the complete chromosome 3, will that make a difference in the results?
In other words again :D , I want to know if each snps is treated independently...
thanks for helping me,

[changed to [SOLVED] based on last post -- Yurii]
Manon Bernard
Laboratory of Cardiovascular physiology and genetics Physiology and
Experimental Medicine The Hospital for Sick Children Toronto

Maksim Struchalin
Posts: 4
Joined: Tue Feb 08, 2011 8:16 pm

Re: probABEL palinear --mmscore function.

Postby Maksim Struchalin » Tue Feb 08, 2011 8:42 pm

Hello Manon,

When you run ProbABEL with --mmscore option you make association analysis with correction on family relationships for each single SNP independently. If you would like to split your genotype data for several portions what you only should carry about is that your iversed variance-covariance matrix is calculated based on all snps (or sufficientnumer of them >10.000?). So, if this matrix stays the same then you can break the data on as many portions as you would like.

yurii
GenABEL developer
GenABEL developer
Posts: 263
Joined: Fri Jan 21, 2011 5:20 pm

Re: probABEL palinear --mmscore function.

Postby yurii » Tue Feb 08, 2011 9:04 pm

small note: if you want to run in parallel in the most effective way, you better make use of DatABEL format (supported by latest ProbABELs, e.g. 0.1-9c) which operates in extremely low RAM mode and allows fast access to arbitrary parts of the data
Note that (Gen)ABELs are dynamically developing; while this post is intended to provide full information at the time of posting, please read on further posts, if any, as the topic may be updated with novel solutions at a later stage.

best regards,
Yurii

manonb
GenABEL suite user
GenABEL suite user
Posts: 23
Joined: Mon Feb 07, 2011 3:47 pm

Re: probABEL palinear --mmscore function.

Postby manonb » Wed Feb 09, 2011 7:55 pm

Thanks Maskim and Yuli,

just a small note: the purpose running palinear with smaller chunk is rather because I did imputation with the IMPUTE software and it's best if we impute by region of 5mbp,due to memory consumption. So I just kept the resulting files in chunk format throughout the whole pipeline, until palinear. so I just run 500-600 palinears, all in parallel... :shock:
so I am happy with your answer, no need to reorganise my data for concatening them in chroms...
thanks again!

--Manon.
Manon Bernard
Laboratory of Cardiovascular physiology and genetics Physiology and
Experimental Medicine The Hospital for Sick Children Toronto


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