After generating the params file, I get the following error when creating the sql database from the Skyline file:
> ### Run AvG
> library(AvantGardeDIA)
> AvantGardeDIA::AvantGardeDIA_InChunks_DB(D.file.name = D.file.name,RefinementWorkflow = "GlobalRefinement")
-- Column specification --------------------------------------------------------
cols(
.default = col_character(),
IsDecoy = col_logical(),
PrecursorCharge = col_double(),
PrecursorMz = col_double(),
ProductCharge = col_double(),
ProductMz = col_double(),
Quantitative = col_logical(),
LibraryDotProduct = col_double(),
MinStartTime = col_double(),
MaxEndTime = col_double(),
Area = col_double(),
LibraryIntensity = col_double()
)
i Use `spec()` for the full column specifications.
Error in data.frame(u, Start_ID_Analyte = unique(D$Data$ID_Analyte)[1], :
arguments imply differing number of rows: 1, 0
Calls: <Anonymous> -> data.frame
In addition: Warning message:
The `...` argument of `group_keys()` is deprecated as of dplyr 1.0.0.
Please `group_by()` first
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Execution halted
I am running Skyline 21.1.0.146 and installed AvantGarde 0.0.1.5 from the tools store. Note that the AvantGarde R package was not installed automatically and I had to install it manually (R 4.0.3 was installed by Skyline).