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tonywu1999 merged 2 commits into from
Sep 17, 2025
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docs(fragpipe): Modify vignettes to include global profiling run example #119

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docs(fragpipe): Modify vignettes to include global profiling run example
tonywu1999 Sep 17, 2025
f792022
update documentation to show if theres no global profiling run
tonywu1999 Sep 17, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -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
18 changes: 13 additions & 5 deletions R/converters.R
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Expand Up @@ -241,25 +241,33 @@ 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$PTM)
#'
#' # If no global profiling run is available, omit input_protein and set:
#' # msstats_data = FragPipetoMSstatsPTMFormat(input, annot,
#' # label_type = "LF", mod_id_col = "STY",
#' # localization_cutoff = .75, protein_id_col = "ProteinName",
#' # peptide_id_col = "PeptideSequence", use_unmod_peptides = FALSE)
#'
#' # Note that this is NULL because we did not include a global profiling run.
#' # Ideally, you should include an independent global profiling run.
#' head(msstats_data$PTM)
#' head(msstats_data$PROTEIN)
#'
FragPipetoMSstatsPTMFormat = function(input,
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97 changes: 97 additions & 0 deletions inst/tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv
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@@ -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
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,4,JCI_230921_TiO2-phos85D_1660,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,55273.465
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,27288.379
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,56355.08
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,23782.973
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_1338,30869.537
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,3,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,30077.96
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
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,1,3-9-2023_JCI_230308_DDA_TiO2-10L_S1-A5_199,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,2,CR_Tio2-WT_1715,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,1,CR_Tio2-phos85D_1716,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,3,JCI-TiO2-DDAphosMethod-WT_1338,19424.299
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,2,JCI-TiO2-DDAphosMethod-rho_1339,NA
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,WT,4,JCI-TiO2-DDAstd-WT_1335,18153.773
sp|P02400|RLA4_YEAST,FATVPTGGASSAAAGAAGAAAGGDAAEEEKEEEAKEESDDDMGFGLFD,4,NA,NA,L,MUT,3,JCI-TiO2-DDAstd-rho_1336,NA
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
18 changes: 13 additions & 5 deletions man/FragPipetoMSstatsPTMFormat.Rd
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10 changes: 8 additions & 2 deletions vignettes/MSstatsPTM_LabelFree_Workflow.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
```


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