Entering edit mode
6.6 years ago
eduardorazza
•
0
Hi, I'm learning basic GWAS analysis using the Foulkes lab tutorial available at http://www.stat-gen.org
The thing is that just cannot read the PLINK files. Following the tutorial I have used the code:
geno <- read.plink(gwas.fn$bed, gwas.fn$bim, gwas.fn$fam, na.strings = ("-9"))
But I repeatedly get the following error:
Error in read.plink(gwas.fn$bed, gwas.fn$bim, gwas.fn$fam, na.strings = ("-9")) :
Couldn't open input file: ~/Desktop/GWAStutorial.bed
As it looks like I just can't open the .bed file, which contains the genotype information, coded in binary. But the file is the exactly one from the tutorial, available to anyone. Any chance it might be corrupted?
Anybody can give me any hints?
Thanks in advance!
what is the output of
?
I set the output dir the same as the data.dir. Would this be a problem? o.0
what is the output of
?
Erro: '/' inesperado in "head(~/"
Where "Erro" means "Error" and "inesperado" means "unexpected".
Português? - eu falo da forma fluente o português.
The
headcommand will not be able to interpret a binary file but it should still output something.It is good practice to always use full absolute paths for files, e.g., /home/eduardorazza/Escritorio/GWAStutorial.bed
On that note, is it because, on your computer, 'Desktop' is actually 'Escritorio'? It seems that you are using a Portuguese locale.
Kevin
Hey! Thanks Kevin! I just reset it, deleted and started it all over setting the Desktop as my directory and output directory to simplify things. It turned out that now it just worked. Also i did it in a different network, but I don't know if this could have affected the previous failure. O que você acha, Kevin? De qualquer maneira, muito obrigado pelo retorno! Abraço! :-)
De nada amigo, abraços!