shubham1637 / dialignr Goto Github PK

Hi,
a new problem has appeared. I always get the message:

Error in (function (classes, fdef, mtable) :
cannot find inherited method for function 'dbGetQuery' for signature '"mzRpwiz", "character"'.

library(DIAlignR)
dataPath <- "/Users/.../Documents/Paper/try"
params <- paramsDIAlignR()
params[["runType"]] <- "DIA_Metabolomics"
params[["context"]] <- "experiment-wide"
params[["chromFile"]] <- 'mzML'
alignTargetedRuns(dataPath = dataPath, outFile = "test.csv", runs = NULL, oswMerged = TRUE, params = params)
Looking for merged.osw file.
13 runs are in merged.osw file
13 .chrom.mzML files are found.
Following runs will be aligned:
[1] "180712_PS-B1-3-101" "180712_PS-B1-3-103" "180712_PS-B1-3-20"
[4] "180712_PS-B1-3-46" "180712_PS-B1-3-48" "180712_PS-B1-3-90"
[7] "18625_PS-B1-109" "18625_PS-B1-117" "18625_PS-B1-119"
[10] "18625_PS-B1-130" "18625_PS-B1-133" "18625_PS-B1-134"
[13] "18625_PS-B1-136"
405 precursors are found.
The execution time for getting precursors:
Time difference of 0.01578689 secs
5265 peptides scores are fetched.
The execution time for fetching peptide scores:
Time difference of 1.004398 secs
Calculating reference run for each peptide.
The execution time for calculating a reference run:
Time difference of 0.07623196 secs
19 peakgroups are found below 0.05 FDR in run 180712_PS-B1-3-101, ID = 4048074721523380537
....
The execution time for fetching features:
Time difference of 0.5495172 secs
Collecting metadata from mzML files.
Metadata is collected from mzML files.
The execution time for getting pointers:
Time difference of 5.518783 secs
Collecting chromatogram indices for all precursors.

Fetched chromatogram indices from /Users/adrianbrun/Documents/Paper/try/xics/18625_PS-B1-136.chrom.mzML
The execution time for getting chromatogram indices:
Time difference of 1.560749 secs
Building multipeptide.
405 peptides are in the multipeptide.
The execution time for building multipeptide:
Time difference of 3.863176 secs
Calculating global alignments.
Geting global alignment of run10 and run0,Increasing maxFdrGlobal 10 times
n = 10
Geting global alignment of run10 and run1,Increasing maxFdrGlobal 10 times
n = 7

Geting global alignment of run6 and run12,Increasing maxFdrGlobal 10 times
n = 10
The execution time for calculating global alignment:
Time difference of 0.3936419 secs
Performing reference-based alignment.
Processing Batch 1
Error in (function (classes, fdef, mtable) :
cannot find inherited method for function 'dbGetQuery' for signature '"mzRpwiz", "character"'.

Sorry for all the questions, however I am not very familiar with R... . Is this error message due to me?

Many greetings

Is it possible to change the assumed chromatogram files folder to something more general? Like xics or chromatograms? Because I usually store my sqMass files in a folder called sqmass, not mzml since they're not mzML files, which causes an issue with get_filenames.R#L84.

It's not a problem to just rename the folder to mzml, more so just a personal preference..

getLOESSfit returns an uninformative error when using non-optimal maxGlobalFdr for loess fit.

Error in vecseq(f__, len__, if (allow.cartesian || notjoin || !anyDuplicated(f__,  : 
  Join results in 5359 rows; more than 5228 = nrow(x)+nrow(i). Check for duplicate key values in i each of which join to the same group in x over and over again. If that's ok, try by=.EACHI to run j for each group to avoid the large allocation. If you are sure you wish to proceed, rerun with allow.cartesian=TRUE. Otherwise, please search for this error message in the FAQ, Wiki, Stack Overflow and data.table issue tracker for advice.

There is a check that increments the maxGlobalFdr by 10 times get_global_fit.R#L246, but in my case I had to decrease the FDR to 0.01 for one run pair, and even further 0.006 for another run pair. Might need to implement another check that decrements maxGlobalFdr.

Whether MRM data is supported now?