Hello,
Sorry but, what doesn't work? What is the error message or result?
As for stringsAsFactors not keeping character strings as character
strings maybe this is from calling data.frame from within the
environment used by with(), but you can use other ways of converting to
character strings, such as
mod5.sig$snps <- as.character(mod5.sig$snps)
before subsetting. And you can also check the result of
colnames(todos) %in% mod5.sig$snp
What does this give you?
Hope this helps,
Rui Barradas
Em 24-10-2012 11:58, Silvano Cesar da Costa escreveu:
Hi,
still doesn't work.
Hello,
I've just seen the error, you are _not_ searching for colnames in
mod5.sig$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
---------------------------------------------
---------------------------------------------
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.
