Search found 36 matches

by MariaG
Tue Feb 08, 2011 11:53 am
Forum: GenABEL
Topic: [SOLVED] "convert.snp.ped" for Plink-formatted file: a bug?
Replies: 3
Views: 4214

[SOLVED] "convert.snp.ped" for Plink-formatted file: a bug?

Hi :) I have plink files: *.ped, *.map, *.phen Example (not real data): ped: FAMILY-PT-9H4M PT-9H4M 0 0 2 -9 C C FAMILY-PT-9H86 PT-9H86 0 0 2 -9 A C FAMILY-PT-9HBA PT-9HBA 0 0 1 -9 C C FAMILY-PT-9H87 PT-9H87 0 0 2 -9 C C ... map: 0 SNP_A-8282305 0 554484 0 SNP_A-8282312 0 554636 0 SNP_A-8282315 0 55...
by MariaG
Tue Feb 08, 2011 11:14 am
Forum: GenABEL
Topic: [SOLVED] Convert from GenABEL into PLINK format
Replies: 5
Views: 2929

Re: Convert from GenABEL into PLINK format

And anyway, I just wonder, if Family-info is saved somewhere among GenABEL's variables?
by MariaG
Tue Feb 08, 2011 11:12 am
Forum: GenABEL
Topic: [SOLVED] Convert from GenABEL into PLINK format
Replies: 5
Views: 2929

Re: Convert from GenABEL into PLINK format

Unfortunatelly, "export.plink" doesn't work - I always get an error message, which asks to close the R session. I would suppose, it's still a "memory problem".
In somedays I plan to install Linux-64, will see if the function will wok there..
by MariaG
Mon Feb 07, 2011 10:12 am
Forum: GenABEL
Topic: [SOLVED] Convert from GenABEL into PLINK format
Replies: 5
Views: 2929

[SOLVED] Convert from GenABEL into PLINK format

Hi :) Is there easy possibility to convert back to PLINK format from the GenABEL? I'm trying to compose plink.ped file manually, based on GenABEL dataset. However I can't find how to reconstract a family-structure (family,id,mo,fa)? For example, with gwaa.data@phdata$id I can get only individual ids...
by MariaG
Mon Feb 07, 2011 8:44 am
Forum: GenABEL
Topic: [SOLVED] Formula for polygenic(), qtscore(), mlreg()
Replies: 4
Views: 6628

Re: Formula for polygenic(), qtscore(), mlreg()

Thank you, Yurii, that's exactly what I need. And thanks for the so detailed model descriptions - important to understand! About mlreg(pheno ~ 1, ...) trick I was thinking, because it's normal for linear models approach. However I was not sure, because in the script you use .C-function, and it's not...
by MariaG
Fri Feb 04, 2011 11:56 am
Forum: GenABEL
Topic: [SOLVED] Formula for polygenic(), qtscore(), mlreg()
Replies: 4
Views: 6628

[SOLVED] Formula for polygenic(), qtscore(), mlreg()

Hello :) I'm trying a very easy task, just to perform GWAS with GenABEL for two models: (1) ph ~ gt (2) ph ~ gt + age Using lm(), I would compose the formula like: lm(ph ~ gt) lm(ph ~ gt + age) But what is a right way to write a formula in polygenic(), qtscore(), mlreg() ? If I understood correctly,...

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