Closed ortizmateujuan closed 3 years ago
The error you show above tells you that you don't have a feature variable named "phenoDisco.Input" in your data set. The features variable used as input for phenotype discovery doesn't have to be name that.
You need to run the phenoDisco()
function from the pRoloc
package to identify new subcellular phenotypes.
You can export your data with the write.expr()
function. In your case, to get all feature variables into a csv file:
write.exprs(ms, fcol = fvarLabels(ms), file = "ms.csv", sep = ",")
Closing the issue, but feel free to re-open this one or create a new one if necessary.
Hi,
I have successfully made a PCA analysis with my SWATH data using the
prolocVis()
function. MiniSWATH.xlsxBut now if I want to run the code to assign new subcellular phenotypes to my data I need to have an Input column in a .csv file with the markers. (Something like the "phenoDisco Input" column in this data): ncomms9992-s2.xlsx
This is the code so far:
Then I want to get the markers
getMarkers(ms, fcol = "phenoDisco.Input")
but I don´t have them added to the .csv file so:
> getMarkers(ms, fcol = "phenoDisco.Input") Error in isMrkVec(object, fcol) : fcol %in% fvarLabels(object) is not TRUE
So, my question is that if it is possible to export this information derived from
addMarkers
into my data .csv file or into a new .csv file. TheprolocVis()
function shows a table with this column but I see no option of exporting this into a .xlsx or .csv.The same question goes for the rest of the
featureData
in the natcomms9992 file: phenoDisco Output, SVM markers, classification... How I add these in to my data?Any help would be appreciated, thanks!