P2df / effAB / effBB as NA

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ImanMEZ
Posts: 5
Joined: Tue Mar 08, 2016 4:28 pm

P2df / effAB / effBB as NA

Postby ImanMEZ » Mon Mar 14, 2016 4:40 pm

Hi,

Can you help clarify the output P-values from mlreg(GASurv()).
The documentation states that the P1df and P2df variables should hold a list of p-values for the allelic and genotypic tests of association, respectively.
so when I run the descriptives.scan(coxresults, top=20) i expect to see P1df and P2df, also effB,effAB and effBB

but my results looks like this

All my effAB, effBB, chi2.2df & P2df are coming as "NA".

Chromosome Position Strand A1 A2 N effB se_effB chi2.1df P1df Pc1df effAB effBB chi2.2df P2df
rs14789 4 94875197 u G A 257 2.0550438 0.4081228 25.35481 4.77E-07 7.16E-07 NA NA NA NA
rs25418 18 567256316 u G A 257 2.603928 0.5395747 23.28921 1.39E-06 2.03E-06 NA NA NA NA
rs12365 18 158723567 u G A 257 2.603928 0.5395747 23.28921 1.39E-06 2.03E-06 NA NA NA NA
rs25896 5 254238742 u G A 256 1.2486798 0.2594778 23.15804 1.49E-06 2.17E-06 NA NA NA NA
rs145236 1 125742548 u C A 257 0.7671174 0.1619584 22.43451 2.17E-06 3.12E-06 NA NA NA NA

is that normal, or me I made some mistake uploading my data into a correct format.

I am running these commands


#Convert to gwaa.data class

convert.snp.tped('data.tped','data.tfam', out='data.out')

survivaldata <- load.gwaa.data(phenofile = "pheno.txt", genofile = "data.out")


#run quality control

qc1 <- check.marker(survivaldata)


qcGWAS <- survivaldata[qc1$idok, qc1$snpok]


#Run cox proportional hazards model

coxresults<- mlreg(GASurv(survivaldata@phdata$ObsMonths, survivaldata@phdata$Status)~survivaldata@phdata$Pheno1, data=qcGWAS)


I am quite new using GenABEL, so still learning to make sense of my results, help is appreciated :)
Thanks very much,

JaneChu
Posts: 2
Joined: Wed Jul 27, 2016 1:08 pm

Re: P2df / effAB / effBB as NA

Postby JaneChu » Wed Jul 27, 2016 1:21 pm

Hi,

I am also new using GenABEL and I am having the same problem.
Did you figure out ??

I was also wondering if the A1 and A2 are the same as is in Plink, however in my results the minor allele is A2 and Ref allele is A1, is that correct?


Thanks in advance!!!

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: P2df / effAB / effBB as NA

Postby lckarssen » Wed Jul 27, 2016 4:04 pm

How many SNPs and how many samples does your analysis have? Do many variants have a low MAF?
-------
Lennart Karssen
PolyOmica
The Netherlands
-------

JaneChu
Posts: 2
Joined: Wed Jul 27, 2016 1:08 pm

Re: P2df / effAB / effBB as NA

Postby JaneChu » Fri Jul 29, 2016 8:40 am

Hi

I have 86 SNPs and 188 samples.
Most of them have low MAF , but even for some of them that has high MAF I still have the same results

One exemple:
Case Control
31/71/41 9/22/14

Chromosome Position Strand A1 A2 N effB se_effB chi2.1df P1df Pc1df effAB effBB chi2.2df P2df
11 27680744 u A T 186 -0.15464889 0.2089636 5.48E-01 0.459254124 0.499966514 NA NA NA NA


Best

Janete


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