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tonywu1999 merged 3 commits into from
Jul 28, 2025
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docs(Philosopher): Add examples for using Philosopher/Fragpipe converter #90

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5a8d34b
docs(Philosopher): Add examples for using Philosopher/Fragpipe converter
tonywu1999 Jul 28, 2025
2d14c46
remove rows from annotation
tonywu1999 Jul 28, 2025
c52c9e6
add unit tests
tonywu1999 Jul 28, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -23,4 +23,4 @@ Encoding: UTF-8
LazyData: true
URL: http://msstats.org/msstatstmt/
BugReports: https://groups.google.com/forum/#!forum/msstats
RoxygenNote: 7.3.1
RoxygenNote: 7.3.2
10 changes: 10 additions & 0 deletions R/converters.R
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Expand Up @@ -332,6 +332,16 @@ SpectroMinetoMSstatsTMTFormat <- function(
#'
#' @return `data.frame` of class `MSstatsTMT`
#'
#' @examples
#' input_file_path = system.file("raw_data/Philosopher/msstats.csv",
#' package = "MSstatsTMT")
#' annotation_file_path = system.file("raw_data/Philosopher/MSstatsTMT_annotation.csv",
#' package = "MSstatsTMT")
#' input = data.table::fread(input_file_path)
#' annotation = data.table::fread(annotation_file_path)
#' msstats_format = PhilosophertoMSstatsTMTFormat(input, annotation)
#' head(msstats_format)
#'
#' @export
PhilosophertoMSstatsTMTFormat = function(
input, annotation, protein_id_col = "Protein",
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4 changes: 2 additions & 2 deletions R/utils_MSstatsTMT.R
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Expand Up @@ -13,9 +13,9 @@
#' \item \code{\link{groupComparisonTMT}} : tests for significant changes in protein abundance across conditions.
#' }
#'
#' @docType package
#' @name MSstatsTMT
NULL
#' @keywords internal
"_PACKAGE"


#' Example of output from Proteome Discoverer 2.2 for TMT-10plex experiments.
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61 changes: 61 additions & 0 deletions inst/raw_data/Philosopher/MSstatsTMT_annotation.csv
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@@ -0,0 +1,61 @@
Run,Fraction,TechRepMixture,Mixture,Channel,BioReplicate,Condition
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01,1,1,plex16,126,CPT0088900003_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f02,2,1,plex16,126,CPT0088900003_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f03,3,1,plex16,126,CPT0088900003_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01,1,1,plex16,127N,CPT0079270003_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f02,2,1,plex16,127N,CPT0079270003_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f03,3,1,plex16,127N,CPT0079270003_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01,1,1,plex16,127C,CPT0088920001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f02,2,1,plex16,127C,CPT0088920001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f03,3,1,plex16,127C,CPT0088920001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01,1,1,plex16,128N,CPT0079300001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f02,2,1,plex16,128N,CPT0079300001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f03,3,1,plex16,128N,CPT0079300001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01,1,1,plex16,128C,CPT0088550004_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f02,2,1,plex16,128C,CPT0088550004_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f03,3,1,plex16,128C,CPT0088550004_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01,1,1,plex16,129N,QC6_QC,QC
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f02,2,1,plex16,129N,QC6_QC,QC
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f03,3,1,plex16,129N,QC6_QC,QC
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01,1,1,plex16,129C,CPT0014450004_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f02,2,1,plex16,129C,CPT0014450004_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f03,3,1,plex16,129C,CPT0014450004_T,T
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01,1,1,plex16,130N,CPT0088570001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f02,2,1,plex16,130N,CPT0088570001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f03,3,1,plex16,130N,CPT0088570001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01,1,1,plex16,130C,CPT0014470001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f02,2,1,plex16,130C,CPT0014470001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f03,3,1,plex16,130C,CPT0014470001_N,N
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f01,1,1,plex16,131N,pool16_NORM,Norm
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f02,2,1,plex16,131N,pool16_NORM,Norm
16CPTAC_CCRCC_W_JHU_20180322_LUMOS_f03,3,1,plex16,131N,pool16_NORM,Norm
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,126,CPT0006730001_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,126,CPT0006730001_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,126,CPT0006730001_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,127N,CPT0069190001_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,127N,CPT0069190001_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,127N,CPT0069190001_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,127C,CPT0092730003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,127C,CPT0092730003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,127C,CPT0092730003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,128N,CPT0092740003_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,128N,CPT0092740003_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,128N,CPT0092740003_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,128C,QC7_QC,QC
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,128C,QC7_QC,QC
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,128C,QC7_QC,QC
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,129N,CPT0006630003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,129N,CPT0006630003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,129N,CPT0006630003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,129C,CPT0025920001_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,129C,CPT0025920001_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,129C,CPT0025920001_N,N
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,130N,CPT0025880003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,130N,CPT0025880003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,130N,CPT0025880003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,130C,CPT0069160003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,130C,CPT0069160003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,130C,CPT0069160003_T,T
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f01,1,1,plex17,131N,pool17_NORM,Norm
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f02,2,1,plex17,131N,pool17_NORM,Norm
17CPTAC_CCRCC_W_JHU_20180517_LUMOS_f03,3,1,plex17,131N,pool17_NORM,Norm
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