[R] How to create a data set from object/data frame?

[Spencer Brackett]

Sarah,

Thank you for the reference to ?data. Upon further research into the
matter, I think I can provide a simpler explanation than the one previously
provided. I am trying to reproduce the following code with an object --
'anno' -- in my data frame/environment.

  >fake.data <- matrix(rnorm(8*200), ncol=8)

I found the number of columns with >ncol(anno)  , which is 3

How do I find rnorm when I don't have the data table (saved as the 'anno'
object) mean or standard dev. ?

I will try reading in the data object through read.table() now, though
won't that just print the data or a subset thereof into my R console?



On Fri, Jul 19, 2019 at 10:46 AM Spencer Brackett <
spbrackett20 using saintjosephhs.com> wrote:

> Sarah,
>
>   I am trying to extract phenoData (ie sample information) from the object
> as part of a procedure to analyze my array for probe sets, which I realize
> is under the BioConducter package Biobase and not relevant to this mailing
> list.
>
>   Yes the original procedure uses data from the Dilution dataset hosted in
> the AffyBatch package affydata. Previous to this part of the procedure, a
> dataset was create via..
>
>   >fake.data <- matrix(rnorm(8*200), ncol=8)
> ##Then phenotype (sample) data was generated in this example through... ##
>
>   sample.info <- data.frame( + spl=paste('A', 1:8, sep=''), +
> stat=rep(c('cancer' , 'healthy'), each=4))
>
> ##Then a meta data.frame object was created to give more intelligible
> labels##
>
> > meta.info <- data.frame (labelDescription = + c('Sample Name' , 'Cancer
> Status')) Then we put them all together: > pheno <-
> new("AnnotatedDataFrame", + data = sample.info, + varMetadata = meta.info
> )
>
> ##Which was then aggregated together##
>
> > pheno <- new("AnnotatedDataFrame", + data = sample.info, + varMetadata
> = meta.info)
>
>   >my.experiments <- new("ExpressionSet", + exprs=fake.data,
> phenoData=pheno)
>    > my.experiments
> ExpressionSet (storageMode: lockedEnvironment) assayData: 200 features, 8
> samples element names: exprs
>
> ##The following deals with further manipulating the phenoData##
> phenoData
>    sampleNames: 1, 2, ..., 8 (8 total) varLabels and varMetadata
> description: spl: Sample Name stat: Cancer Status
>
> featureData
>  featureNames: 1, 2, ..., 200 (200 total) fvarLabels and fvarMetadata
> description: none
> experimentData:  use 'experimentData(object)'
> Annotation:
>
> ##At this point is when the dataset 'Dilution was read in through
> data(Dilution)
>
> which was made an object of the AnnotatedDataFrame via
>
> >phenoData(Dilution)
>
> My apologies in advance as I know the above info. pertains to functions
> carried out strictly through BioConducor, but is the only context I can
> provide for what I am trying to do.
>
> Best,
>
> Spencer
>
>
> On Fri, Jul 19, 2019 at 10:23 AM Sarah Goslee <sarah.goslee using gmail.com>
> wrote:
>
>> Hi Spencer,
>>
>> Your description doesn't make any sense to me. If anno is already an R
>> object, what are you trying to do with it?
>>
>> data() is for loading datasets that come with packages; if your object
>> is already an R object in your environment, then there's no need for
>> it.
>>
>> It sounds like you are possibly working through an example provided
>> elsewhere, that has sample data loaded with data(). If so, then you do
>> not need that step for your own data. You just need to import it into
>> R in the correct format.
>>
>> If that doesn't help, then I think we need more information on what
>> you're trying to do.
>>
>> Sarah
>>
>> On Fri, Jul 19, 2019 at 10:18 AM Spencer Brackett
>> <spbrackett20 using saintjosephhs.com> wrote:
>> >
>> > Hello,
>> >
>> >   I am trying to create a data set from an object called ‘anno’ in my
>> > environment. I’ve tried arguments like saveRDS(anno, file = “”) and
>> > save(anno, file “.RData”) to save the object as a file to see if that
>> will
>> > work, but it seems for the particular procedure I am trying to carry
>> out, I
>> > need to transpose the object to a data set. Any ideas as to how I might
>> do
>> > this? For reference, my next step in manipulating the data contained in
>> the
>> > object is data(), which evidently does not work for reading in data
>> frame
>> > objects as data(“file/object name).
>> >
>> > Best,
>> >
>> > Spencer
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > 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.
>>
>>
>>
>> --
>> Sarah Goslee (she/her)
>> http://www.numberwright.com
>>
>

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