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Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(SpectroPipeR) ################# Welcome to ##################### _____ _ _____ _ _____ | __|___ ___ ___| |_ ___ ___| _ |_|___ ___| __ | |__ | . | -_| _| _| _| . | __| | . | -_| -| |_____| _|___|___|_| |_| |___|__| |_| _|___|__|__| |_| |_| ##################################################### version: 0.3.0 > > > # use_test("SpectR_test_all") > > test_check("SpectroPipeR") #***************************************** # READ SPECTRONAUT MODULE #***************************************** checking parameters ... loading data ... write input data to output folder ... R.FileName capping ... create folder: 02_ID_rate/8_sample_analysis generating intermediate SDRF file saving intermediate SDRF file ... please use https://lessdrf.streamlit.app for finalizing/editing file before submitting to a public repository _________ data set loaded with ... _________ number of raw files = 8 number of conditions = 2 number of ions without filtering = 1095 number of peptides without filtering = 904 number of Protein groups without filtering = 93 count profiled values ... performing counting of min. sample percentage where an ion was detected... ion Q-value cutoff < 0.001 12.5 % (1/8) is the min. sample percentage where an ion was detected performing ID rate filtering ... performing protein count over replicates (more than or equal 2 peptides) ... performing protein count (<2 and more than or equal 2 peptides) ... _________ ON/OFF analysis: _________ ... filter with Q-value 0.001 ... ... filter for 2 peptides and min. present in 50% of replicates ... ... ON/OFF analysis write outputs ... count missed cleavages ... save missed cleavage plots... _________ ID rate per sample: _________ ions: median = 971.5; min. = 933; max. = 1003 modified peptides: median = 856; min. = 825; max. = 878 stripped peptides: median = 815; min. = 785; max. = 836 protein groups: median = 91; min. = 87; max. = 93 read module done --> please check outputs in folder: D:\temp\RtmpKG16mf/02_ID_rate/ #***************************************** # NORMALIZATION & QUANTIFICATION MODULE #***************************************** sorting Replicates and conditions ... NORMALIZATION WAS DONE IN SPECTRONAUT... ...skipping normalization step and use Spectronaut normalized data instead... save Normalization factor plot ... save Normalization boxplot ... generate ion CV data... save ion CV data plots... save ion CV data vs. mean intensity hexbin plots... calculating peptide intensity data ... writing peptide intensity data ... filter Met_oxidized peptides ... TRUE 60 Met_oxidized peptides filtered for quantification replacing 0.0139821029082774 % of values (ZERO quantity values) with 0.5 = half-minimal value protein intensity calculation ... extracting iBAQ intensities from Spectronaut report ... calc. mean, SD, CV of iBAQ intensities ... ... save iBAQ data ... perform maxLFQ protein intensity calculation ... (this will take some time) ... preprocessing data for MaxLFQ estimation ... Concatenating secondary ids... Removing low intensities... ... generate protein list for MaxLFQ estimation ... # proteins = 93, # samples = 8 5.4% 11% 16% 22% 27% 32% 38% 43% 48% 54% 59% 65% 70% 75% 81% 86% 91% 97% Completed. ... calculation of MaxLFQ ... 5.4% 11% 16% 22% 27% 32% 38% 43% 48% 54% 59% 65% 70% 75% 81% 86% 91% 97% Completed. ... generate outputs for MaxLFQ estimation ... ... do median normalization of MaxLFQ data ... ... save MaxLFQ boxplot ... ... save MaxLFQ data ... ... compare protein intensities and iBAQ protein intensities ... ... 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[========================================================== ] 97.03% - calculation ... [=========================================================== ] 98.02% - calculation ... [=========================================================== ] 99.01% - calculation ... [============================================================] 100.00% - calculation ... ... render CV plot ... generating raw file / condition file ... no outlier detected with 4 fold difference from the median norm. & quant. module done --> please check outputs in folder: D:\temp\RtmpKG16mf/03_normalization/ norm. & quant. module done --> please check outputs in folder: D:\temp\RtmpKG16mf/05_processed_data/ #***************************************** # MVA MODULE #***************************************** perfoming multivariate analysis ... generating raw file / condition file ... PCA analysis on peptide level ... PCA analysis on protein level ... ... 0 proteins removed due to NAs generating Scree plots ... generating Top10 variable contribution plot ... generating 3D PCA plot ... generating PCA plot 1st vs. 2nd dimension ... generating PCA plot 1st to 5th dimension ... saving PCA plot 1st to 5th dimension ... generating Biplot of Top10 variables and individuals ... generating individuals contribution plot ... generating PCA plot matrix ... saving PCA plot matrix ... saving 3D PCA plots ... performing correlation analysis ... performing correlation analysis - calculate p-values ... generating correlation plots ... saving correlation plots ... saving correlation plots with condition info ... perform UMAP analysis on protein level ... try UMAP with default settings ... due to low complexity try UMAP with n_neighbors = 5 setting ... MVA module done --> please check outputs in folder: D:\temp\RtmpKG16mf/04_multivariate_analysis/ #***************************************** # STATISTICS MODULE #***************************************** reformatting data ... register processor cores ... performing statistical analysis (this might take a while) ... | | | 0% | |======================================================================| 100% close cores ... start to end time comparison for stat. analysis: 0.00205410692426893 hours estimating effect sizes ... [============================================================] 100.00% - calc. effect sizes... join and tidy tables ... filtering statistical table using supplied cutoffs ... writing output files ... adding iBAQ quantiles to statistics table ... generating Excel outputs ... performing fold-change cutoff sensitivity analysis ... plotting fold-change cutoff sensitivity analysis ... [================================================================================] 100.00% - 1 plotting fold-change simple cutoff sensitivity analysis (peptide n > 1)... [================================================================================] 100.00% - 1 generating volcano plots ... [============================================================] 100.00% - Volcano plots with adj. p-value [============================================================] 100.00% - Volcano plots with adj. p-value [============================================================] 100.00% - Volcano plots with raw p-value condition-comparison-wise signal to noise comparison ... ...signal to noise: save scatter plot... condition-comparison-wise comparison of peptide-int.-ratios vs. protein-int.-ratios ... ...calculating protein ratios... ...combining ratio tables... ...generating ratio-ratios: protein_ratios/peptide_ratios... ...filter for at least 2 peptides... ...adding of protein intensity to table... ...add signal to noise per group... ...add detection with selected q-value cutoff with at least 2 peptides per replicate... ...add direction comparison for protein or peptide condition comp. ratio... ...save table of stat. significant with poor signal to noise... ...counting protein which having a 2fold difference... ...select Top15 over- or under-estimated proteins... ...protein int. benchmark: save scatter plot... ...protein int. benchmark: save histogram plot... ...protein int. benchmark: save table... ...counting protein: gradient of difference... ...protein int. benchmark: gradient of difference area plots... statistics module done --> please check outputs in folder: D:\temp\RtmpKG16mf/06_statistics/ [ FAIL 0 | WARN 449 | SKIP 1 | PASS 0 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-SpectR_test_all.R:3:1' [ FAIL 0 | WARN 449 | SKIP 1 | PASS 0 ] > > proc.time() user system elapsed 103.50 5.81 117.07