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

[Spencer Brackett]

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]]
> >
> > ______________________________________________
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>
>
>
> --
> Sarah Goslee (she/her)
> http://www.numberwright.com
>

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