Error in Preprocessing Function
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