[BioC] Scan not respecting what
mtmorgan at fhcrc.org
Thu Aug 26 19:20:51 CEST 2010
On 8/26/2010 10:10 AM, Gaston Fiore wrote:
> 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’
> 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?
In the usage section it shows
scan(file = "", what = double(0), nmax = -1, n = -1, sep = "",
and in the Details we have
The type of 'what' or its components can be one of the six atomic
vector types or 'NULL' (see 'is.atomic').
where 'type of' suggests
but these are definitely obscure, and inconsistent with, e.g.,
read.table, where colClasses is a character vector naming the types of
> 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
>>>>  "character"
>>>>  "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.
>>>> Thanks a lot,
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor