From 64800fa564762d7e76a2bf4981bbe3b5329328ed Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Tue, 16 Sep 2025 21:52:49 -0400 Subject: [PATCH 1/2] docs(fragpipe): Modify vignettes to include global profiling run example --- DESCRIPTION | 2 +- R/converters.R | 11 ++- .../raw_data/Fragpipe/msstats_proteome_lf.csv | 97 +++++++++++++++++++ man/FragPipetoMSstatsPTMFormat.Rd | 11 ++- vignettes/MSstatsPTM_LabelFree_Workflow.Rmd | 10 +- 5 files changed, 118 insertions(+), 13 deletions(-) create mode 100644 inst/tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv diff --git a/DESCRIPTION b/DESCRIPTION index 167a0fe..8b31d05 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -40,5 +40,5 @@ biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, DifferentialE BugReports: https://github.com/Vitek-Lab/MSstatsPTM/issues Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Config/testthat/edition: 3 diff --git a/R/converters.R b/R/converters.R index fbcde23..8b6510b 100644 --- a/R/converters.R +++ b/R/converters.R @@ -241,25 +241,26 @@ DIANNtoMSstatsPTMFormat = function(input, #' head(msstats_data$PTM) #' head(msstats_data$PROTEIN) #' -#' # LFQ Example (w/out global profiling run) +#' # LFQ Example #' input = system.file("tinytest/raw_data/Fragpipe/MSstats.csv", #' package = "MSstatsPTM") #' input = data.table::fread(input) #' annot = system.file("tinytest/raw_data/Fragpipe/experiment_annotation.tsv", #' package = "MSstatsPTM") -#' annot = data.table::fread(annot) +#' annot = data.table::fread(annot) +#' input_protein = system.file("tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv", +#' package = "MSstatsPTM") +#' input_protein = data.table::fread(input_protein) #' #' msstats_data = FragPipetoMSstatsPTMFormat(input, #' annot, +#' input_protein = input_protein, #' label_type="LF", #' mod_id_col = "STY", #' localization_cutoff=.75, #' protein_id_col = "ProteinName", #' peptide_id_col = "PeptideSequence") #' head(msstats_data$PTM) -#' -#' # Note that this is NULL because we did not include a global profiling run. -#' # Ideally, you should include an independent global profiling run. #' head(msstats_data$PROTEIN) #' FragPipetoMSstatsPTMFormat = function(input, diff --git a/inst/tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv b/inst/tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv new file mode 100644 index 0000000..cb648c7 --- /dev/null +++ b/inst/tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv @@ -0,0 +1,97 @@ +ProteinName,PeptideSequence,PrecursorCharge,FragmentIon,ProductCharge,IsotopeLabelType,Condition,BioReplicate,Run,Intensity +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,44400.42 +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,54096.2 +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,42032.559 +sp|O13563|RPN13_YEAST,MIGVLNNSSESDEEESNDEKQK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,45441.47 +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,39071.486 +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,49027.117 +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,25728.36 +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,50606.861 +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,29068.013 +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,48775.5 +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA +sp|O74302|YD13A_YEAST,MESQQLSQHSPISHGSACASVTSK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA +sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA +sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,WT,2,CR_Tio2-WT_1715,35259.795 +sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA +sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA +sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA +sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA +sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA +sp|P00445|SODC_YEAST,FEQASESEPTTVSYEIAGNSPNAER,2,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA +sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA +sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,47090.12 +sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA +sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA +sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA +sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,NA +sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA +sp|P00445|SODC_YEAST,HVGDMGNVKTDENGVAK,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,182842.8 +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,91160.492 +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,121482.805 +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,50779.54 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+sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,NA +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,50823.02 +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,83515.89 +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA +sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA \ No newline at end of file diff --git a/man/FragPipetoMSstatsPTMFormat.Rd b/man/FragPipetoMSstatsPTMFormat.Rd index af7589c..019fc97 100644 --- a/man/FragPipetoMSstatsPTMFormat.Rd +++ b/man/FragPipetoMSstatsPTMFormat.Rd @@ -121,25 +121,26 @@ msstats_data = FragPipetoMSstatsPTMFormat(fragpipe_input, head(msstats_data$PTM) head(msstats_data$PROTEIN) -# LFQ Example (w/out global profiling run) +# LFQ Example input = system.file("tinytest/raw_data/Fragpipe/MSstats.csv", package = "MSstatsPTM") input = data.table::fread(input) annot = system.file("tinytest/raw_data/Fragpipe/experiment_annotation.tsv", package = "MSstatsPTM") -annot = data.table::fread(annot) +annot = data.table::fread(annot) +input_protein = system.file("tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv", + package = "MSstatsPTM") +input_protein = data.table::fread(input_protein) msstats_data = FragPipetoMSstatsPTMFormat(input, annot, + input_protein = input_protein, label_type="LF", mod_id_col = "STY", localization_cutoff=.75, protein_id_col = "ProteinName", peptide_id_col = "PeptideSequence") head(msstats_data$PTM) - -# Note that this is NULL because we did not include a global profiling run. -# Ideally, you should include an independent global profiling run. head(msstats_data$PROTEIN) } diff --git a/vignettes/MSstatsPTM_LabelFree_Workflow.Rmd b/vignettes/MSstatsPTM_LabelFree_Workflow.Rmd index 749b87b..2d2b31c 100644 --- a/vignettes/MSstatsPTM_LabelFree_Workflow.Rmd +++ b/vignettes/MSstatsPTM_LabelFree_Workflow.Rmd @@ -140,22 +140,28 @@ msstats_data = FragPipetoMSstatsPTMFormat(fragpipe_input, head(msstats_data$PTM) head(msstats_data$PROTEIN) -# LFQ Example (w/out global profiling run) +# LFQ Example input = system.file("tinytest/raw_data/Fragpipe/MSstats.csv", package = "MSstatsPTM") input = data.table::fread(input) annot = system.file("tinytest/raw_data/Fragpipe/experiment_annotation.tsv", package = "MSstatsPTM") -annot = data.table::fread(annot) +annot = data.table::fread(annot) +input_protein = system.file("tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv", + package = "MSstatsPTM") + +input_protein = data.table::fread(input_protein) # Global profiling run msstats_data = FragPipetoMSstatsPTMFormat(input, annot, + input_protein = input_protein, label_type="LF", mod_id_col = "STY", localization_cutoff=.75, protein_id_col = "ProteinName", peptide_id_col = "PeptideSequence") head(msstats_data$PTM) +head(msstats_data$PROTEIN) ``` From f792022a11c8af6a37f5bb3f07ad2673648f0f27 Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Wed, 17 Sep 2025 08:54:37 -0400 Subject: [PATCH 2/2] update documentation to show if theres no global profiling run --- R/converters.R | 7 +++++++ man/FragPipetoMSstatsPTMFormat.Rd | 7 +++++++ 2 files changed, 14 insertions(+) diff --git a/R/converters.R b/R/converters.R index 8b6510b..108cc41 100644 --- a/R/converters.R +++ b/R/converters.R @@ -260,6 +260,13 @@ DIANNtoMSstatsPTMFormat = function(input, #' localization_cutoff=.75, #' protein_id_col = "ProteinName", #' peptide_id_col = "PeptideSequence") +#' +#' # If no global profiling run is available, omit input_protein and set: +#' # msstats_data = FragPipetoMSstatsPTMFormat(input, annot, +#' # label_type = "LF", mod_id_col = "STY", +#' # localization_cutoff = .75, protein_id_col = "ProteinName", +#' # peptide_id_col = "PeptideSequence", use_unmod_peptides = FALSE) +#' #' head(msstats_data$PTM) #' head(msstats_data$PROTEIN) #' diff --git a/man/FragPipetoMSstatsPTMFormat.Rd b/man/FragPipetoMSstatsPTMFormat.Rd index 019fc97..17402a9 100644 --- a/man/FragPipetoMSstatsPTMFormat.Rd +++ b/man/FragPipetoMSstatsPTMFormat.Rd @@ -140,6 +140,13 @@ msstats_data = FragPipetoMSstatsPTMFormat(input, localization_cutoff=.75, protein_id_col = "ProteinName", peptide_id_col = "PeptideSequence") + +# If no global profiling run is available, omit input_protein and set: +# msstats_data = FragPipetoMSstatsPTMFormat(input, annot, +# label_type = "LF", mod_id_col = "STY", +# localization_cutoff = .75, protein_id_col = "ProteinName", +# peptide_id_col = "PeptideSequence", use_unmod_peptides = FALSE) + head(msstats_data$PTM) head(msstats_data$PROTEIN)