Check the read.table help (hint: check.names), which points you to the 'make.names' function... that's why. Cheers, Cei On 6/27/11 6:05 PM, Changbin Du wrote: > Hi, Valerie, > > Thanks for the reply! > > Yes, now I can successfully extract the columns I want with the required.col > argument as long as the > required.col<- c("A{5}A", "A{5}F"). The read.columns works fine. > > > IF I use* read.table*, however, even the original column names are ("A{5}A", > "A{5}F" etc), I still get A.5.D" "A.5.F" "A.5.G" etc. I dont know how > it happens. > > Anyway, the read.columns work for me now. > > Thanks for all the helps! > > > > > On Mon, Jun 27, 2011 at 3:58 PM, Valerie Obenchain<vobencha at="" fhcrc.org="">wrote: > >> ** >> On 06/27/2011 08:51 AM, Changbin Du wrote: >> >> HI, Valerie, >> >> Thanks for the information! >> >>> >> hh.full<-read.columns("/house/homedirs/c/cdu/operon/gh/dd.dimer",re quired.col=NULL, >> sep="\t", skip=0, quote="", fill=T) >>> colnames(hh.full) >> [1] "gene_id" "A{5}A" "A{5}C" "A{5}D" "A{5}E" "A{5}F" "A{5}G" >> >> * >> My variables names are right and same as my original file(dd.dimer)* >> >> But when I use the following codes: >>> dimer.hh<-read.table("/house/homedirs/c/cdu/operon/gh/dd.dimer", >> sep="\t", skip=0, quote="", header=T, fill=T) >>> colnames(dimer.hh) >> [1] "gene_id" "A.5.A" "A.5.C" "A.5.D" "A.5.E" "A.5.F" "A.5.G" >> >> >> The variables names changed. the { } are changed to .. , I dont know how? >> >> >> I'm not sure why you are seeing the parenthesis replaced by periods. I have >> tested your example on a sample file of my own where I named the columns >> "A{5}A", "A{5}C" etc. and I can not replicate this behavior. The columns >> names in the result are the same regardless if I use the required.col=NULL >> or leave it out. >> >> More importantly, have you been successful in extracting the columns you >> want with the required.col argument now that you know how the column names >> appear? For example, >> >> required.col<- c("A{5}A", "A{5}F") >> >> >> Valerie >> >> >> Thanks! >> >> >> >> >> >> On Mon, Jun 27, 2011 at 7:02 AM, Valerie Obenchain<vobencha at="" fhcrc.org="">wrote: >> >>> Hi Changbin, >>> >>> Looking at the documentation for read.columns in the limma package, the >>> required.col argument should select the columns you want. >>> >>> It looks like you were successful in reading in all of the data on your >>> first try. Check the column names in that file to be sure they match the >>> names you are inputting with the variable "var". For example, >>> >>> myfile<- "/house/homedirs/c/cdu/operon/gh/dd.dimer" >>> hh_full<- read.columns(myfile, quote="") >>> colnames(hh) >>> >>> You should see the column names you expect, then try selecting the columns >>> with >>> >>> var<-c("a1", "c1", "a11", "b11", "f111") >>> hh_reduced<- read.columns(myfile, required.col=var, quote="") >>> >>> Valerie >>> >>> >>> >>> >>> >>> >>> >>> >>> On 06/24/11 15:21, Changbin Du wrote: >>> >>>> Dear Bioconductor community, >>>> >>>> I am using your read.columns to read some columns into R, I found the >>>> >>>> >>>>> following problems, can you help me? >>>>> >>>>> I have a large data set names dd.txt, the *columns* are: there are 2402 >>>>> variables. >>>>> >>>>> a1, b1, ..z1, a11, b11, ...z11, a111, b111, ..z111.. >>>>> >>>>> IF I dont know the *relative* position of the *columns*, but I know I >>>>> need >>>>> the >>>>> following variables: >>>>> var<-c(a1, c1,a11,b11,f111) >>>>> >>>>> Can I *use* *read*.*columns* *to* *read* the data *into* *R*? >>>>> >>>>> I have tried the following codes, but it does not work >>>>> >>>>> hh<-*read*.*columns*("/house/homedirs/c/cdu/operon/gh/dd.dimer", >>>>> *required*.col=NULL, text.*to*.search=var, sep="\t", skip=0, quote="", >>>>> fill=T) >>>>> >>>>> dim(hh) >>>>> 468, 2402 >>>>> >>>>> >>>>> hh<-*read*.*columns*("/house/homedirs/c/cdu/operon/gh/dd.dimer", >>>>> *required*.col=var, text.*to*.search="", sep="\t", skip=0, quote="", >>>>> fill=T) >>>>> >>>>> dim(hh) >>>>> 0, 0 >>>>> >>>>> Thanks so much! >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> >> >> >> -- >> Sincerely, >> Changbin >> -- >> >> Changbin Du >> DOE Joint Genome Institute >> Bldg 400 Rm 457 >> 2800 Mitchell Dr >> Walnut Creet, CA 94598 >> Phone: 925-927-2856 >> >> >> >> > >