[BioC] Scan not respecting what

Martin Morgan mtmorgan at fhcrc.org
Thu Aug 26 07:00:38 CEST 2010


  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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>
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