Search found 12 matches

by marcin
Wed Dec 10, 2014 3:06 pm
Forum: GenABEL
Topic: HELP file genotype.raw phenotype.raw
Replies: 1
Views: 1086

Re: HELP file genotype.raw phenotype.raw

Hi Marco! I am one of the authors of this tutorial. I was quite a while ago and the tutorial was a part of a LUPA (an EU consortium aiming at studying dog genetics) workshop. The data was proprietary at the time and we could use it only within LUPA. I still have to formally ask whether the data can ...
by marcin
Sun Jan 27, 2013 6:31 pm
Forum: GenABEL
Topic: [SOLVED] SNP position issue
Replies: 3
Views: 1842

Re: SNP position issue

Hi Mateo, 1. The dataset you are using is not a real canine data. It is simulated based on canine-data, but chromosomes were shuffled and renamed if I remember correctly. It was explicitly stated during the workshop, but not mentioned in the tutorial. I will have a more careful look, but it is most ...
by marcin
Tue May 08, 2012 8:38 am
Forum: GenABEL
Topic: [SOLVED]convert.snp.ped issue with missing val. @ 1st marker
Replies: 4
Views: 3761

convert.snp.ped issue with missing val. @ 1st marker

Apparently there is yet another problem. We see it when using --dog option in PLINK to produce per and map files. If any of the individuals has 0 (missing value) at the first marker, GenABEL returns error. Dirty remedy to this is to introduce some fake monomorphic first marker, but I think it should...
by marcin
Wed Mar 28, 2012 10:03 am
Forum: GenABEL
Topic: conver.snp.tped
Replies: 9
Views: 4599

Re: conver.snp.tped

Hi, UPDATE: It actually turned out that the reading error was caused by specifying path in a relative way. Weird anyway... using in convert.snp.ped ~kiero/Research/AtopyGSD/data/atopy.ped ---- more often works ~/Research/AtopyGSD/data/atopy.ped ---- sometimes works /Users/kiero/Research/AtopyGSD/dat...
by marcin
Wed Mar 14, 2012 7:51 pm
Forum: GenABEL
Topic: loading data
Replies: 1
Views: 1185

Re: loading data

Hi Mark,

the best would be to use PED (or TPED) and MAP files as described here: http://pngu.mgh.harvard.edu/~purcell/pl ... .shtml#ped

To get help on at a loading, type ?load.gwaa.data in R terminal. Hope this helps,

Marcin
by marcin
Wed Mar 14, 2012 7:49 pm
Forum: GenABEL
Topic: Summary of more than top 10 SNPs
Replies: 1
Views: 1163

Re: Summary of more than top 10 SNPs

Hi, the lines below should solve your problem. For more refer to GenABEL help, e.g. by typing name of the function with question mark suffix: ?descriptives.scan More complex help you can find here: http://rgm2.lab.nig.ac.jp/RGM2/search.php?query=GenABEL Hope this helps, Martin an0 <- qtscore(qt2,dat...
by marcin
Mon Feb 13, 2012 12:16 pm
Forum: GenABEL
Topic: [SOLVED]convert.snp.ped issue with missing val. @ 1st marker
Replies: 4
Views: 3761

Re: convert.snp.ped issue with missing value at the first ma

Actually found now a related post, but it seems that it still does not solve the problem...
viewtopic.php?f=6&t=592
by marcin
Mon Feb 13, 2012 9:18 am
Forum: GenABEL
Topic: MDS plot
Replies: 1
Views: 1373

Re: MDS plot

Hej Hille,

is there any symmetry relationship between the two MDSes? I have seen an MDS that in the later version of GenABEL became its own mirror picture.

Marcin
by marcin
Mon Feb 13, 2012 9:16 am
Forum: GenABEL
Topic: Polygenic function: problem of conversion
Replies: 1
Views: 1480

Re: Polygenic function: problem of conversion

Try using polygenic_hglm function instead:

Code: Select all

hglm <- polygenic_hglm(myTrait, data.gkin, data)
an.mm <- mmscore(hglm, data)


Hopefully this helps!

Martin
by marcin
Wed Feb 08, 2012 12:06 pm
Forum: GenABEL
Topic: [SOLVED]convert.snp.ped issue with missing val. @ 1st marker
Replies: 4
Views: 3761

[SOLVED]convert.snp.ped issue with missing val. @ 1st marker

Hi, Version: GenABEL 1.6-9 My ped file: CFA001772 CFA001772 CFA001772 CFA001772 -9 2 0 0 G G My map file: chr rsid cM bp 1 BICF2G630707759 0 3014448 1 BICF2S2358127 0 3068620 My code: convert.snp.ped(pedfile="Research/Behaviour project/data/head.ped", mapfile="Research/Behaviour proje...

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