... Thank you very much for the bug report. The issue wasn't in `phenoDisco` itself (which used the appropriate feature variable), but a helper function (`anyUnknown`) that performed some test and that didn't get the user's `fcol` passed along.
The issue is fixed in version 1.25.2 that is available im ...
... You can use the respective accessors to extract these information from the object. Below, I use the `serine` object created in the [`MSnbase` *centroiding* vignette](http://lgatto.github.io/MSnbase/articles/v03-MSnbase-centroiding.html):
List of 6
$ F1.S628: n ...
... Below, I have the `chrs` object as created in `?Chromatograms`. It is possible to extract the retention time and intensities from individual chromatogram composing the `Chromatograms` with `rtime` and `intensity`:
Chromatograms with 2 rows and 2 columns
... The previous post to refer to is different than you issue. In your case, unfortunately, the `addIdentificationData` will not work as it expects to find information that it can't find when reading data from an `mgf` file. This code was written for the more complete `mzML` format in mind.
What you ca ...
... This is most likely due to the fact that the precursor M/Z isn't exactly 808.5253. 808.5253 is probably a rounded up value that is shown as part of showing the spectrum object, and `==` returns `TRUE` when the two values are exactly identical. You would need to check the exact value of the M/Z value ...
... I have the following `DataFrame`
> k <- sample(3, 10, replace = TRUE)
> df <- DataFrame(k = k,
+ x = round(rnorm(length(k)), 2),
+ y = seq_len(length(k)),
+ z = sample(LETTERS, length(k), replace = TRUE),
+ ir = IRange ...
... Strange, and unlikely to be an `MSnbase` issue. Could you
1. restart R altogether
2. re-install with `BiocManager::install("MSnbase")`
3. load `library("MSnbase")`
If the above fails, could you provide the end of the installation output. ...