[R] factor or character

[Silvano Cesar da Costa]

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 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
>> ---------------------------------------------
>>
>
>
>


---------------------------------------------
Silvano Cesar da Costa

Universidade Estadual de Londrina
Centro de Ciências Exatas
Departamento de Estatística

Fone: (43) 3371-4346