[BioC] Scan not respecting what

[Gaston Fiore]

Thanks Martin, now it gives integers. Why isn't this in the described in the R Documentation, however? From there:

    what: the type of ‘what’ gives the type of data to be read.  The
          supported types are ‘logical’, ‘integer’, ‘numeric’,
          ‘complex’, ‘character’, ‘raw’ and ‘list’.  If ‘what’ is a
          list, it is assumed that the lines of the data file are
          records each containing ‘length(what)’ items (‘fields’) and
          the list components should have elements which are one of the
          first six types listed or ‘NULL’, see section ‘Details’
          below.

I don't see anywhere that I should specify 1L as opposed to 'integer', even though that seems to be the correct way of achieving what I wanted since it works. Any comments?

Thanks,

-Gaston


On Aug 26, 2010, at 1:00 AM, Martin Morgan wrote:

> On 8/25/2010 9:57 PM, Martin Morgan wrote:
>> On 8/25/2010 9:21 PM, Gaston Fiore wrote:
>>> Hello everyone,
>>> 
>>> By some (strange to me) reason, scan isn't respecting the what argument:
>>> 
>>>> temp<- scan(file = "~/data/WT/NS20WTR1ChrReadsF.txt", what = 'integer', sep = ",", quote = 'NULL', comment.char = "")
>>> Read 26042606 items
>>>> class(temp)
>>> [1] "character"
>>>> typeof(temp)
>>> [1] "character"
>>> 
>>> I'm new to R, and I apologize if the mistake is obvious, but could someone explain to me why this is the case?
>> Hi Gaston --
>> 
>> The 'what' argument is an instance of the data type to be parsed, so what=integer() or what=1.
> 
> That last should be what=1L; the  'L' is R's way of saying that the whole number should be an integer rather than a numeric. Martin
>> 
>> Hope that helps.
>> 
>> Martin
>>> Thanks a lot,
>>> 
>>> -Gaston
>>> 
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>