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

Questions about GenABEL (aka *ABEL) suite of packages
Forum rules
Please remember not to post any sensitive data on this public forum.
The first few posts of newly registered users will be moderated in order to filter out any spammers.

When get a solution to the problem you posted, please change the topic name (e.g. from "how to ..." to "[SOLVED] how to ..."). This will make it easier for the community to follow the posts yet to be attended.
marcin
GenABEL suite user
GenABEL suite user
Posts: 12
Joined: Wed Feb 09, 2011 10:03 am

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

Postby marcin » Wed Feb 08, 2012 12:06 pm

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:

Code: Select all

convert.snp.ped(pedfile="Research/Behaviour project/data/head.ped", mapfile="Research/Behaviour project/data/head.map", outfile="Research/Behaviour project/data/head.raw")

Error:
Reading map from file 'Research/Behaviour project/data/head.map' ...
... done. Read positions of 1 markers from file 'Research/Behaviour project/data/head.map'
Reading genotypes from file 'Research/Behaviour project/data/head.ped' ...
...done. Read information for 1 people from file 'Research/Behaviour project/data/head.ped'
Analysing marker information ...
Error in convert.snp.ped(pedfile = "Research/Behaviour project/data/head.ped", :
coding '' for SNP not recognised !

After changing ped to:
CFA001772 CFA001772 CFA001772 CFA001772 -9 2 G G 0 0

error disappears.

After trying with tped and team, I got:
Error in convert.snp.tped(tpedfile = "Research/Behaviour project/data/recoded.tped", :
coding '�Ŀ_�' for SNP not recognised !


The first marker can't be missing? Feature, bug or I am doing something wrong? Regards,

Marcin
Last edited by marcin on Wed Mar 14, 2012 7:55 pm, edited 1 time in total.

marcin
GenABEL suite user
GenABEL suite user
Posts: 12
Joined: Wed Feb 09, 2011 10:03 am

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

Postby marcin » Mon Feb 13, 2012 12:16 pm

Actually found now a related post, but it seems that it still does not solve the problem...
viewtopic.php?f=6&t=592

Nicola Pirastu
GenABEL senior expert
GenABEL senior expert
Posts: 151
Joined: Wed Feb 09, 2011 3:24 pm

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

Postby Nicola Pirastu » Tue Feb 14, 2012 10:21 pm

Hi,

the probelm is not the coding of the missing value (It would have told you three alleles for SNP xxxx) but the name of the SNP, for some reason its supposed to be rs*. Try changing the marker names to rs* and everything should go fine.
I really have no idea why the code is set this way and to me it seems like a bug and a really annoying one since the error message is a bit misterious.

Best

Nicola

marcin
GenABEL suite user
GenABEL suite user
Posts: 12
Joined: Wed Feb 09, 2011 10:03 am

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

Postby marcin » Tue May 08, 2012 8:38 am

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 be addressed in the new GenABEL releases.

lhare
Posts: 1
Joined: Wed Apr 02, 2014 2:42 pm

Re: [SOLVED]convert.snp.ped issue with missing val. @ 1st ma

Postby lhare » Wed Apr 02, 2014 2:56 pm

Thank you for this! I am having exactly this problem! --dogs! I wouldn't have guessed that. I have

Debian Linux R 2.15.1, GenABEL 1.8-0
Windows R 3.0.1, GenABEL 1.8-0
PLINK 1.07

Thanks for posting a workaround!


Return to “GenABEL”

Who is online

Users browsing this forum: No registered users and 1 guest