[R] How to extract information from .Rdata format

[Rui Barradas]

Hello,

Inline.

Às 05:30 de 01/08/2020, Ana Marija escreveu:
> do you think that this is useful output from Basics of R?

Actually, the answer will be yes, I do. Explanation follows.

>> load("paired_example.Rdata")
>> str(rawdata)
>   num [1:4482, 1:10] 46 4 3 48 1 4 0 60 0 12 ...
>   - attr(*, "dimnames")=List of 2
>    ..$ : chr [1:4482] "gene1" "gene2" "gene3" "gene4" ...
>    ..$ : chr [1:10] "a.cancer" "b.cancer" "c.cancer" "d.cancer" ..

This says that rawdata is a numeric matrix with 4482 rows and 10 columns.
And that an useful attribute, dimnames, is set.

>
> I think this one is better:
>> dat<-local(get(load("paired_example.Rdata")))
>> head(dat)
>        a.cancer b.cancer c.cancer d.cancer e.cancer a.normal b.normal c.normal
> gene1       46        4       33        5        8       61        5       42
> gene2        4        0        2        1        5       24        1       30
> gene3        3        4        4        2        1        3        0        0
> gene4       48        2       10        0        6        9        4        3
> gene5        1        5        2        3        6        1        0        3
> gene6        4        0        0        1        1        4        0        7

This gives a better *visual* representation of the data, rawdata is an 
object of class "matrix" and it now *looks* like a table. We are used to 
seeing matrices printed like this so it's very easy to understand what 
rawdata is about.
Note that this one only has 8 columns, did you process the data before 
calling head()?

Anyway, why not run both str(rawdata) and head(rawdata)? Not only I 
don't see a conflict, they are even complementary to one another.

As for the original question, Sarah did answer to it, when you load() a 
.Rdata or .RData file the objects are created in a certain environment 
and their names are returned, you don't need get(), it's redundant.

Hope this helps,

Rui Barradas
>
> On Fri, Jul 31, 2020 at 11:05 PM Bert Gunter <bgunter.4567 using gmail.com> wrote:
>> Sarah has explained all.
>>
>> I agree with her about the need for tutorials also. This list cannot substitute for such homework on your own.
>>
>> Bert Gunter
>>
>> "The trouble with having an open mind is that people keep coming along and sticking things into it."
>> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>>
>>
>> On Fri, Jul 31, 2020 at 7:55 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>>> Hi Bert,
>>>
>>> it gives me this:
>>>
>>>> a=load("paired_example.Rdata")
>>>> str(a)
>>>   chr [1:3] "rawdata" "treatment" "patient"
>>>
>>> I don't know how to extract "treatment" for example in a data frame.
>>>
>>> I tried this but of no help.
>>>> b=a[[2]]
>>>> b
>>> [1] "treatment"
>>>
>>>> str(treatment)
>>>   chr [1:10] "treat" "treat" "treat" "treat" "treat" "control" "control" ...
>>>
>>> but this is not the format I need.
>>>
>>> On Fri, Jul 31, 2020 at 9:18 PM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>>>> Hello,
>>>>
>>>> I have this file:
>>>>> a=load("paired_example.Rdata")
>>>>> a
>>>> [1] "rawdata"   "treatment" "patient"
>>>>
>>>> I can extract "rawdata" with:
>>>>   dat<-local(get(load("paired_example.Rdata")))
>>>>
>>>> Can you please advise how would I extract in data frame "treatment"
>>>> and "patient"?
>>>>
>>>> Thanks
>>>> Ana
>>> ______________________________________________
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> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


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