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Error in Preprocessing Function

Open LarryMe27 opened this issue 7 months ago • 2 comments

Hi together, I used this code and wanted to skip preprocessing:


library(HiTMaP)

datafile=c("Data/kidney_Lme033.imzML")
wd="D:/data/Larissa/R_proj/"


preprocess = list(force_preprocess=FALSE,
                  use_preprocessRDS=TRUE)

imaging_identification(datafile=paste0(wd,datafile),
                       trehold=0.5,
                       ppm=20,
                       Digestion_site="trypsin",
                       missedCleavages=0:1,
                       Fastadatabase="Maus_2024_05_15.fasta",
                       adducts= c("M+H"),
                       Decoy_mode = "isotope",
                       mzrange=c(800,2000),
                       parallel=12,
                       Segmentation="spatialKMeans",
                       preprocess = preprocess,
                       Region_feature_summary = TRUE,
                       score_method="SQRTP",
                       Protein_feature_summary = TRUE,
                       plot_ion_image = TRUE,
                       Peptide_feature_summary = TRUE)

I got this returned: 224 Cores detected, 4 threads will be used for computing 1 files were selected and will be used for Searching Maus_2024_05_15.fasta was selected as database. Candidates will be generated through Proteomics mode Found enzyme: trypsin Found rule: "" Found customized rule: "" Testing fasta sequances for degestion site: (KR)|((?<=W)K(?=P))|((?<=M)R(?=P)) Generated 54910 Proteins in total. Computing exact masses... Generating peptide formula... Generating peptide formula with adducts: M+H Calculating peptide mz with adducts: M+H Candidate list has been exported. Maus_2024_05_15.fasta was selected as database Spectrum intensity threshold: 0.10% mz tolerance: 20 ppm Segmentation method: spatialKMeans Manual segmentation def file: None Bypass spectrum generation: FALSE Found rotation info Loading raw image data for statistical analysis: kidney_Lme033.imzML parsing imzML file: ‘D:\data\Larissa\R_proj\Data\kidney_Lme033.imzML’ detected 'processed' imzML creating MSImagingExperiment applying profile m/z-values to all spectra using mass.range 800 to 2000 using resolution 5 ppm binning intensity from mz 800 to 1999.9985 with relative resolution 5e-06 returning MSImagingExperiment done. Preparing image data for statistical analysis: kidney_Lme033.imzML Error in if (preprocess$smoothSignal$method == "Disable") { : argument is of length zero

Could you please help me with this? Thanks in advance

LarryMe27 avatar Apr 30 '25 08:04 LarryMe27