Entering edit mode
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 ?
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$Sepal.Length > 7, 1]@data Sepal.Length 103 7.1 106 7.6 108 7.3 110 7.2 118 7.7 119 7.7 123 7.7 126 7.2 130 7.2 131 7.4 132 7.9 136 7.7Yes, but shouldn't the usual column accessor work?
Ah I see. This is what I get:
Which explains at least why it is not working (you get similar for for tmp[1,]). I guess the idea is that subsetting with `[` should return an `AnnotatedDataFrame` object, but accessing directly with `$` gets you the values. I have no idea if this is the intended behavior.The philosophy is that
[is an 'endomorphism' -- it returns the class as it is applied to.$and[[are not. Also, usepData()rather than slot access, and (strongly) considerS4Vectors::DataFramefor a more modern implementation of theAnnotatedDataFrameconcept.Thanks! Why is pData() preferred over slot access?
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.
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:
Maybe I misunderstood and when you said "pData() rather than slot access" you meant example 3 here?
Yes, I meant example 3; the
@datain C: Comparison of Column of AnnotatedDataFrame is slot access. tmp$Sepal.Length; pData(tmp)$Sepal.Legnth;pData(tmp[,"Sepal.Length"])$Sepal.Length etc would be acceptable, as with[[.I see! I completely forgot I used the slot to access the data for checking in my original example. Now I have no idea why I did that on the first place. I have updated that comment to avoid misleading potential readers. Thank you!
And this works also:
One more thought. I guess this behavior is also consistent with that of `data.frame(..., drop = FALSE)`. `[` will always return a data.frame, whereas `$` and `[[` return a vector.
It would be nice if there was a section of documentation titled Accessors.