R help - Oct 2012 - factor or character

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 Ci?ncias Exatas
Departamento de Estat?stica

Fone: (43) 3371-4346

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 Ci?ncias Exatas
> Departamento de Estat?stica
>
> Fone: (43) 3371-4346
>
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