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.