[R] factor or character

[Silvano Cesar da Costa]

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 at 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