Comparison of Column of AnnotatedDataFrame
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Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 4 days ago
Australia

The documentation example of AnnotatedDataFrame are quite limited and only show how to coerce between data.frame and AnnotatedDataFrame. How can I subset a column of an AnnotatedDataFrame and check for equality to a particular value, without converting it to a data.frame first, for example ?

biobase AnnotatedDataFrame • 2.3k views
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Sorry if I am missing the point but do you mean something different from this?:

library(Biobase)

tmp <- AnnotatedDataFrame(iris)

tmp[, 1] # select first column.
#tmp[, 1]@data # this is bad idea- see comments below.
pData(tmp)[, 1] # check.

# select rows based on value of one column:
tmp[tmp$Sepal.Length > 7, 1]@data

    Sepal.Length
103          7.1
106          7.6
108          7.3
110          7.2
118          7.7
119          7.7
123          7.7
126          7.2
130          7.2
131          7.4
132          7.9
136          7.7
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Yes, but shouldn't the usual column accessor work?

> tmp[, "Sepal.Length"] > 7
Error in tmp[, "Sepal.Length"] > 7 :
  comparison (6) is possible only for atomic and list types
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Ah I see. This is what I get:

> tmp[, "Sepal.Length"]
An object of class 'AnnotatedDataFrame'
  rowNames: 1 2 ... 150 (150 total)
  varLabels: Sepal.Length
  varMetadata: labelDescription
Which explains at least why it is not working (you get similar for for tmp[1,]). I guess the idea is that subsetting with `[` should return an `AnnotatedDataFrame` object, but accessing directly with `$` gets you the values. I have no idea if this is the intended behavior.
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The philosophy is that [ is an 'endomorphism' -- it returns the class as it is applied to. $ and [[ are not. Also, use pData() rather than slot access, and (strongly) consider S4Vectors::DataFrame for a more modern implementation of the AnnotatedDataFrame concept.

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Thanks! Why is pData() preferred over slot access?

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The 'usual' reasons for object-oriented programming -- it separates the user-oriented interface from design considerations employed by the developer. Often not much divergence but for instance the slots (internal developer business) of a DNAStringSet have little to do with the interface designed for the user.

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Sorry if I look persistent on this but I didn't consider using $ or [[ as slot access. But maybe I am mistaken? I see (at least) three ways to access the data in the example above:

tmp$Sepal.Length # use subsetting method.
pData(tmp)$Sepal.Length # use accessor method then subsetting method.
tmp@data$Sepal.Length # use slot- bad.

Maybe I misunderstood and when you said "pData() rather than slot access" you meant example 3 here?

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Yes, I meant example 3; the @data in C: Comparison of Column of AnnotatedDataFrame is slot access. tmp$Sepal.Length; pData(tmp)$Sepal.Legnth; pData(tmp[,"Sepal.Length"])$Sepal.Length etc would be acceptable, as with [[.

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I see! I completely forgot I used the slot to access the data for checking in my original example. Now I have no idea why I did that on the first place. I have updated that comment to avoid misleading potential readers. Thank you!

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And this works also:

tmp[["Sepal.Length"]] > 7
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One more thought. I guess this behavior is also consistent with that of `data.frame(..., drop = FALSE)`. `[` will always return a data.frame, whereas `$` and `[[` return a vector.

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It would be nice if there was a section of documentation titled Accessors.

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Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 4 days ago
Australia
anAnnotatedDataFrame[["columnName"]] == value
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