Hello,
I've just seen the error, you are _not_ searching for colnames in
mod5.sig$snps. Corrected:
Selec = todos[ , colnames(todos) %in% mod5.sig$snps]
Hope this helps,
Rui Barradas
Em 23-10-2012 21:17, Silvano Cesar da Costa escreveu:
Hi Rui,
it doesn't work:
(mod5.sig = with(mod5, data.frame(snps = SNP[pvalor<5e-8],
stringsAsFactors=FALSE)))
str(mod5.sig)
'data.frame': 76 obs. of 1 variable:
$ snps: Factor w/ 220 levels "rs10058955_A",..: 89 59 88 73 40 35 97 55
87 204 ...
Selec = todos[ , colnames(todos) %in% mod5.sig]
head(Selec)
data frame com 0 colunas e 6 linhas
the problem is the same.
Thanks,
Hello,
When creating the data.frame of snps use the option stringsAsFactors =
FALSE
I believe your error comes from the fact that you are trying to find
colnames in a variable coded as integers (a factor, like str shows).
Hope this helps,
Rui Barradas
Em 23-10-2012 19:02, Silvano Cesar da Costa escreveu:
Hi,
The program below work very well.
(snps = c('rs621782_G', 'rs8087639_G', 'rs8094221_T', 'rs7227515_A',
'rs537202_C'))
Selec = todos[ , colnames(todos) %in% snps]
head(Selec)
But, I have a data set with 1.000 columns and I need extract 70 to use
(like snps in command above).
This 70 snps are in a file. So I create a file to extract them with
(mod5.sig = with(mod5, data.frame(snps = SNP[pvalor < 5e-8])))
str(mod5.sig)
(snps = (mod5.sig))
The structure is:
'data.frame': 76 obs. of 1 variable:
$ snps: Factor w/ 220 levels "rs10058955_A",..: 89 59 88 73 40 35 97
55
87 204 ...
But it doesn't work. The output is:
Selec = todos[ , colnames(todos) %in% snps]
head(Selec)
data frame with 0 columns and 6 rows
What's is wrong?
Thanks a lot,
---------------------------------------------
Silvano Cesar da Costa
Universidade Estadual de Londrina
Centro de Ciências Exatas
Departamento de Estatística
Fone: (43) 3371-4346
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
---------------------------------------------
Silvano Cesar da Costa
Universidade Estadual de Londrina
Centro de Ciências Exatas
Departamento de Estatística
Fone: (43) 3371-4346
---------------------------------------------
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
