Post by kzar0004 on Aug 13, 2016 12:14:22 GMT
Dear All,
I am new to GCTA and have been trying to use the program to estimate the variance in my phenotypes (e.g. BMI, IQ scores from various cognitive tests) from n=202 subjects explained by my SNPs ( approximately 571074).
My data is in the Binary PED files (plink.bed, plink.bim, and plink.fam).
I started off with this command:
gcta_mac --bfile Danes181_NoMind --autosome --make-grm --out Danes181_NoMind
And then tried to do REML analysis using the GRM from the previous command above using this command:
gcta_mac --grm Danes181_NoMind --pheno Danes197.Noheader --reml --out Danes181_NoMind
But then I receive this output
Reading IDs of the genetic relationship matrix (GRM) from [Danes181_NoMind.grm.id].
181 IDs read from [Danes181_NoMind.grm.id].
Reading the GRM from [Danes181_NoMind.grm.gz].
Pairwise genetic relationships between 181 individuals are included from [Danes181_NoMind.grm.gz].
Error: can not open the file [Danes197.Noheader] to read.
My phenotype file has no header, is a text file, and the columns are: family id, individual id, phenotype...
What am I doing incorrect?
I look forward to your response.
Best wishes,
K
I am new to GCTA and have been trying to use the program to estimate the variance in my phenotypes (e.g. BMI, IQ scores from various cognitive tests) from n=202 subjects explained by my SNPs ( approximately 571074).
My data is in the Binary PED files (plink.bed, plink.bim, and plink.fam).
I started off with this command:
gcta_mac --bfile Danes181_NoMind --autosome --make-grm --out Danes181_NoMind
And then tried to do REML analysis using the GRM from the previous command above using this command:
gcta_mac --grm Danes181_NoMind --pheno Danes197.Noheader --reml --out Danes181_NoMind
But then I receive this output
Reading IDs of the genetic relationship matrix (GRM) from [Danes181_NoMind.grm.id].
181 IDs read from [Danes181_NoMind.grm.id].
Reading the GRM from [Danes181_NoMind.grm.gz].
Pairwise genetic relationships between 181 individuals are included from [Danes181_NoMind.grm.gz].
Error: can not open the file [Danes197.Noheader] to read.
My phenotype file has no header, is a text file, and the columns are: family id, individual id, phenotype...
What am I doing incorrect?
I look forward to your response.
Best wishes,
K
