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[#6045] Using --mmscore and --interaction will not output a column with cov_SNP_int_SNP_covariate

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Date:
2015-03-06 17:23
Priority:
3
State:
Closed
Submitted by:
Lennart Karssen (lckarssen)
Assigned to:
Nobody (None)
Resolution:
Accepted As Bug
Operating System:
All
Severity:
normal
Hardware:
All
Version:
PA v0.4.4
Component:
ProbABEL
URL:
 
Summary:
Using --mmscore and --interaction will not output a column with cov_SNP_int_SNP_covariate

Detailed description
This was reported several times in the forum:

http://forum.genabel.org/viewtopic.php?f=10&t=830&p=1662
http://forum.genabel.org/viewtopic.php?f=10&t=896
http://forum.genabel.org/viewtopic.php?f=10&t=885&p=1881

Some test output:
../src/palinear -p testphenommscore.phe -d inputfiles/mmscore_gen.dose.fvi -i inputfiles/mmscore_gen.mlinfo -o lck2 --mmscore=inputfiles/mmscore_InvSigma_aj.sex.age.dat --interaction=1
probabel v. 0.4.4
(C) Yurii Aulchenko, Lennart C. Karssen, Maarten Kooyman, Maksim Struchalin, The GenABEL team, EMC Rotterdam

Using EIGEN version 3.2.0 for matrix operations
Options in effect:
--pheno = testphenommscore.phe
--info = inputfiles/mmscore_gen.mlinfo
--dose = inputfiles/mmscore_gen.dose.fvi
(using FVF data)
--ntraits = 1
--ngpreds = 1
--interaction = 1
--interaction_only = 0
--mmscore = inputfiles/mmscore_InvSigma_aj.sex.age.dat
--map = not in output
--nids = estimated from data
--chrom = not in output
--out = lck2
--skipd = 2
--separat = " "
--score = OFF
--nohead = OFF
--allcov = OFF
--robust = OFF

Reading info data...
Number of SNPs = 5
Reading phenotype data...
Actual number of people in phenofile = 500; using all of these
Linear model: ( height_residuals ) ~ mu + cov1 + cov2 + SNP_A1 + cov1*SNP_A1
You are running mmscore...
loaded InvSigma...
Reading genotype data... done.
loaded null data... estimated null model... formed regression object...
Analysis: 100.00%... done

Gives:
name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele beta_SNP_addA1 sebeta_SNP_addA1 beta_SNP_cov1 sebeta_SNP_cov1 chi2_SNP_add
rs735579 AC B 0.5847 0.5847 0.5847 0.5847 491 0.534623 1.73386 0.909754 0.296646 1.59171 3.63231
rs9088604 A CTG 0.5847 0.5847 0.5847 0.5847 497 0.435614 -2.07862 0.961285 1.87346 1.6741 4.67569
rs1413801 A B 0.5847 0.5847 0.5847 0.5847 492 0.311992 -2.18676 1.12553 1.20374 1.87225 3.77478
rs4911638 A B 0.5847 0.5847 0.5847 0.5847 496 0.150202 0.675667 1.30507 0.75037 2.25757 0.268039
rs70099 A B 0.5847 0.5847 0.5847 1.2e-17 493 0.0922921 NaN NaN NaN NaN NaN

Followup

Message
Date: 2015-11-04 14:42
Sender: Lennart Karssen

Now that the ProbABEL source code has been moved to Github, this issue will be tracked there: https://github.com/GenABEL-Project/ProbABEL/issues/2

Attached Files:

Changes:

Field Old Value Date By
close_dateNone2015-11-04 14:42lckarssen
status_idOpen2015-11-04 14:42lckarssen
Thanks to:
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