Search found 263 matches

by yurii
Fri Jan 29, 2016 1:26 pm
Forum: GenABEL
Topic: genABEL stratification method
Replies: 2
Views: 1045

Re: genABEL stratification method

Hi, this is very interesting problem you deal with. In short, I would go for full mixed model analysis, not eigenstrat or stratification or anything else - your structure is very complex. Get genomic kinship matrix with 'ibs', estimate polygenic model with 'polygenic' and analyse with 'mmscore'. The...
by yurii
Fri Jun 12, 2015 11:59 am
Forum: GenABEL
Topic: how to install MixABEL correctly?
Replies: 8
Views: 2753

Re: how to install MixABEL correctly?

May be stupid remark - but do you have GSL installed? Also, searching for "MixABEL" in this forum returns a large number of threads, some related to installation problems (e.g. http://forum.genabel.org/viewtopic.php?f=6&t=755&p=1455&hilit=Mixabel#p1455; and few more) - any of t...
by yurii
Fri May 16, 2014 8:55 am
Forum: GenABEL
Topic: How to deal with replicates in inbreeding species (A. th.)
Replies: 8
Views: 5514

Re: How to deal with replicates in inbreeding species (A. th

Would these two be good references? http://arxiv.org/pdf/1010.4681.pdf http://www.journalofdairyscience.org/article/S0022-0302(08)70990-1/fulltext As for division by 2 - this only is done because internally the input matrix is multiplied by 2 :) (we assume that inout is a kinship, not relationship m...
by yurii
Wed Apr 16, 2014 2:22 pm
Forum: Journal Club on Statistical Genomics
Topic: Summer school for statistical omics
Replies: 1
Views: 3966

Summer school for statistical omics

Dear All, I thought that information about the summer school we organize (details below) may be of interest to you. The Summer School for Statistical Omics will be held in Split, Croatia, on August 1 -- 15, 2014 (web-site http://school.statisticalomics.org/). The application deadline was recently ex...
by yurii
Mon Mar 17, 2014 7:32 pm
Forum: GenABEL
Topic: GLM: Capturing stander error (SE) of the estimate
Replies: 8
Views: 2836

Re: GLM: Capturing stander error (SE) of the estimate

I think this goes a bit outside of the topic of this forum towards general R graphical capabilities. In order to fix the graphics bug of scan.glm probably the best place to start with is by reading the source code of plot.scan.gwaa. If you figure out how to fix it, please consider submitting a patch...
by yurii
Fri Mar 14, 2014 2:47 pm
Forum: GenABEL
Topic: GLM: Capturing stander error (SE) of the estimate
Replies: 8
Views: 2836

Re: GLM: Capturing stander error (SE) of the estimate

Here is a quick an ugly fix (please do test!) library(GenABEL) library(GenABEL.data) data(srdta) a <- scan.glm("bt~sex+age+CRSNP",family=binomial(),data=srdta,snps=(1:10),bcast=2) plot(a) # generates an error newMapStaff <- sortmap.internal(a$chromosome,a$map) plot(newMapStaff$cummap,-log1...
by yurii
Wed Mar 12, 2014 10:26 pm
Forum: GenABEL
Topic: GLM: Capturing stander error (SE) of the estimate
Replies: 8
Views: 2836

Re: GLM: Capturing stander error (SE) of the estimate

Error in annotation(object) : trying to get slot "annotation" from an object (class "scan.gwaa") that is not an S4 object and scan.glm produces S3 object. Is this a bug or an intended output from scan.glm? This is a bug. Somebody needs to fix it :) scan.glm is in many ways very ...
by yurii
Wed Mar 12, 2014 10:21 pm
Forum: GenABEL
Topic: GLM: Capturing stander error (SE) of the estimate
Replies: 8
Views: 2836

Re: GLM: Capturing stander error (SE) of the estimate

I don't seem to be able to capture the standard error of the estimate for a SNP effect as a quick fix: you can work SE out from P-values, e.g. if effect B=(-0.1) and p-value P=0.005 then SE of B is B <- (-0.1) P <- 0.005 chi2 <- qchisq(P,df=1,lower=FALSE) SE <- sqrt(B^2/chi2) SE
by yurii
Sun Nov 03, 2013 6:37 pm
Forum: ProbABEL
Topic: how to get 'cov_SNP_int_SNP_covariate' in pedigree analysis
Replies: 3
Views: 2947

Re: how to get 'cov_SNP_int_SNP_covariate' in pedigree analy

In performance, MixABEL is comparable with ProbABEL. It actually used to be even faster, though I am not sure it still holds with recent updates in ProbABEL.

Y
by yurii
Mon Oct 21, 2013 1:41 pm
Forum: ProbABEL
Topic: how to get 'cov_SNP_int_SNP_covariate' in pedigree analysis
Replies: 3
Views: 2947

Re: how to get 'cov_SNP_int_SNP_covariate' in pedigree analy

Dear Qiao,

It seems that you also miss the interaction-beta from the output as well, so basically you are not getting the interaction model to work for you at all. Is this correct?

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