[BioC] question about the read.columns

[Cei Abreu-Goodger]

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",required.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
>>
>>
>>
>>
>
>