From f3d9db0bda3b12e728d70e9b7bf048816fb0ea3f Mon Sep 17 00:00:00 2001 From: Tony Wu Date: Mon, 15 Jul 2024 12:07:42 -0400 Subject: [PATCH] docs(progenesis): Add sample input data from Progenesis for converter --- DESCRIPTION | 2 +- R/converters.R | 25 ++-- .../Progenesis/phospho_annotation.csv | 10 ++ .../Progenesis/progenesis_peptide.csv | 125 ++++++++++++++++++ inst/tinytest/test_converters.R | 17 +++ man/ProgenesistoMSstatsPTMFormat.Rd | 25 ++-- 6 files changed, 179 insertions(+), 25 deletions(-) create mode 100644 inst/tinytest/raw_data/Progenesis/phospho_annotation.csv create mode 100644 inst/tinytest/raw_data/Progenesis/progenesis_peptide.csv diff --git a/DESCRIPTION b/DESCRIPTION index 981bd1d..9eb2a49 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,4 +32,4 @@ biocViews: ImmunoOncology, MassSpectrometry, Proteomics, Software, DifferentialE BugReports: https://github.com/Vitek-Lab/MSstatsPTM/issues Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.2 diff --git a/R/converters.R b/R/converters.R index 7b2cecf..9a6deab 100644 --- a/R/converters.R +++ b/R/converters.R @@ -929,18 +929,19 @@ PDtoMSstatsPTMFormat = function(input, #' required by MSstatsPTM. #' @examples #' -#' # Example annotation file -#' annotation = data.frame('Condition' = c('Control', 'Control', 'Control', -#' 'Treatment', 'Treatment', 'Treatment'), -#' 'BioReplicate' = c(1,2,3,4,5,6), -#' 'Run' = c('prot_run_1', 'prot_run_2', 'prot_run_3', -#' 'phos_run_1', 'phos_run_2', 'phos_run_3'), -#' 'Type' = c("Protein", "Protein", "Protein", "PTM", -#' "PTM", "PTM")) -#' -#' # The output should be in the following format. -#' head(raw.input$PTM) -#' head(raw.input$PROTEIN) +#' input = system.file("tinytest/raw_data/Progenesis/progenesis_peptide.csv", +#' package = "MSstatsPTM") +#' input = data.table::fread(input) +#' colnames(input) = unlist(input[1,]) +#' input = input[-1,] +#' annot = system.file("tinytest/raw_data/Progenesis/phospho_annotation.csv", +#' package = "MSstatsPTM") +#' annot = data.table::fread(annot) +#' prog_imported = ProgenesistoMSstatsPTMFormat( +#' input, +#' annot +#' ) +#' head(prog_imported$PTM) ProgenesistoMSstatsPTMFormat = function(ptm_input, annotation, global_protein_input = FALSE, diff --git a/inst/tinytest/raw_data/Progenesis/phospho_annotation.csv b/inst/tinytest/raw_data/Progenesis/phospho_annotation.csv new file mode 100644 index 0000000..0b264ca --- /dev/null +++ b/inst/tinytest/raw_data/Progenesis/phospho_annotation.csv @@ -0,0 +1,10 @@ +Run,Condition,BioReplicate,Type +001_PH003_G23,A,S1,PTM +002_PH003_G23,B,S2,PTM +003_PH003_G23,A,S3,PTM +004_PH003_G23,A,S4,PTM +005_PH003_G23,B,S5,PTM +006_PH003_G23,B,S6,PTM +007_PH003_G23,C,S7,PTM +008_PH003_G23,C,S8,PTM +009_PH003_G23,C,S9,PTM diff --git a/inst/tinytest/raw_data/Progenesis/progenesis_peptide.csv b/inst/tinytest/raw_data/Progenesis/progenesis_peptide.csv new file mode 100644 index 0000000..01f20f9 --- /dev/null +++ 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SV=1","False","1.39122524218941","B","C","0.327436088817865","37.3237311648108","762993.470538816","1069358.22273555","761890.536210734","1038977.11188908","1332571.81396674","978295.125480823","897316.463887888","1043379.31615233","467141.534688852","473190.272329744","953182.676264969","814641.936354289","1038977.11188908","912977.134776492","1062687.72765357","1022152.56344817","1129963.06703939","614967.787131432","1","0","0","0","0","0","0","0","0" diff --git a/inst/tinytest/test_converters.R b/inst/tinytest/test_converters.R index da1c7ed..c75e47c 100644 --- a/inst/tinytest/test_converters.R +++ b/inst/tinytest/test_converters.R @@ -259,3 +259,20 @@ metamorpheus_imported = MetamorpheusToMSstatsPTMFormat( length(metamorpheus_imported$PTM$PeptideSequence)) .validatePtmSubstring( metamorpheus_imported$PROTEIN, "\\[Common Fixed:Carbamidomethyl on C\\]", 0) + + +# Progenesis +input = system.file("tinytest/raw_data/Progenesis/progenesis_peptide.csv", + package = "MSstatsPTM") +input = data.table::fread(input) +colnames(input) = unlist(input[1,]) +input = input[-1,] +annot = system.file("tinytest/raw_data/Progenesis/phospho_annotation.csv", + package = "MSstatsPTM") +annot = data.table::fread(annot) +prog_imported = ProgenesistoMSstatsPTMFormat( + input, + annot, +) + +.validateProteinId(prog_imported$PTM, "sp|A2ASS6|TITIN_MOUSE_AVTSPPRVKSPEPR_[4] Phospho (ST)|[10] Phospho (ST)", 18) \ No newline at end of file diff --git a/man/ProgenesistoMSstatsPTMFormat.Rd b/man/ProgenesistoMSstatsPTMFormat.Rd index 274b576..5f39c27 100644 --- a/man/ProgenesistoMSstatsPTMFormat.Rd +++ b/man/ProgenesistoMSstatsPTMFormat.Rd @@ -66,16 +66,17 @@ Converts non-TMT Progenesis output into the format needed for MSstatsPTM } \examples{ -# Example annotation file -annotation = data.frame('Condition' = c('Control', 'Control', 'Control', - 'Treatment', 'Treatment', 'Treatment'), - 'BioReplicate' = c(1,2,3,4,5,6), - 'Run' = c('prot_run_1', 'prot_run_2', 'prot_run_3', - 'phos_run_1', 'phos_run_2', 'phos_run_3'), - 'Type' = c("Protein", "Protein", "Protein", "PTM", - "PTM", "PTM")) - -# The output should be in the following format. -head(raw.input$PTM) -head(raw.input$PROTEIN) +input = system.file("tinytest/raw_data/Progenesis/progenesis_peptide.csv", + package = "MSstatsPTM") +input = data.table::fread(input) +colnames(input) = unlist(input[1,]) +input = input[-1,] +annot = system.file("tinytest/raw_data/Progenesis/phospho_annotation.csv", + package = "MSstatsPTM") +annot = data.table::fread(annot) +prog_imported = ProgenesistoMSstatsPTMFormat( + input, + annot +) +head(prog_imported$PTM) }