R Package "example" section of .Rd file question (think it's a non-ASCII issue, but not sure...)
On Feb 15, 2012, at 5:30 PM, Yihui Xie wrote:
Man, the original reply told you to use backticks `` rather than double quotes "". They are very different in R; see ?Quotes And GSE19829-GPL570_eset is really a bad name. I recommend you to rename it. Regards, Yihui -- Yihui Xie <xieyihui at gmail.com> Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Wed, Feb 15, 2012 at 4:09 PM, Ben Ganzfried <ben.ganzfried at gmail.com
wrote: Hi Martin, Thanks! You were right. Quotes seemed to work, except I kept running into a problem on the following line: time <- "GSE19829-GPL570_eset$days_to_death" / 365
If you use Yihui's advice, you should only back-tick around the dataframe name and not around the column name.
The error is that R atomic vector operator invalid.
Because you are trying to divide a character value by a number.
David.
>> It's actually much
>> easier if I could use quotes rather than re-name-- so is there any
>> way to
>> put quotes around the columns in "GSE19829-GPL570_eset" such that
>> it does
>> what i want it to?
>>
>> In the above "time" example, I just want to take the values in the
>> column
>> and divide by 365, but the quotes are messing it up. Any
>> clarification
>> would be really greatly appreciated!
>>
>> Thanks!
>>
>> Ben
>>
>>
>>
>> On Wed, Feb 15, 2012 at 4:20 PM, Martin Morgan <mtmorgan at fhcrc.org>
>> wrote:
>>
>>> On 02/15/2012 12:18 PM, Ben Ganzfried wrote:
>>>
>>>> Hey,
>>>>
>>>> I keep getting the following warning:
>>>>
>>>> data(GSE19829-GPL570_eset)
>>>>>
>>>> Warning in data(GSE19829 - GPL570_eset) :
>>>> data set ?GSE19829 - GPL570_eset? not found
>>>>
>>>>> ## maybe str(GSE19829-GPL570_eset) ; plot(GSE19829-
>>>>> GPL570_eset) ...
>>>>>
>>>>
>>> Hi Ben --
>>>
>>> '-' is being parsed as a minus sign; you could (I think) quote it
>>>
>>> `GSE19829-GPL570_eset`
>>>
>>> or better come up with a legal name.
>>>
>>> Martin
>>>
>>>
>>>>> if(require(affy)){
>>>>>
>>>> + summary(GSE19829-GPL570_eset$**vital_status)
>>>> + }
>>>> Error in summary(GSE19829 - GPL570_eset$vital_status) :
>>>> object 'GSE19829' not found
>>>> Execution halted
>>>>
>>>> This error does not happen on other of my other .Rd files. None
>>>> of the
>>>> other .Rd files have a "-" character in their title. for
>>>> example, the
>>>> other files have the following:
>>>>
>>>>> data(GSE1234)
>>>>>
>>>> OR
>>>>
>>>>> data(GSE5678)
>>>>>
>>>>
>>>> I think the issue is the "-" character, but I'm not sure. Does
>>>> anyone
>>>> know
>>>> if this is the case? And if so, how do I fix it? If not, any
>>>> other
>>>> suggestions?
>>>>
>>>> Much thanks!
>>>>
>>>> Ben
>>>> tained, reproducible code.
David Winsemius, MD
West Hartford, CT