docs(fragpipe): Modify vignettes to include global profiling run example #119
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WalkthroughRoxygenNote in DESCRIPTION bumped. Examples, documentation, and vignette updated to show passing an optional Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant FragPipeConverter as FragPipetoMSstatsPTMFormat
participant OptionalProtein as input_protein (optional)
participant Output as msstats_data
note over User,FragPipeConverter #e6f7ff: Example-level interaction (API call)
User->>FragPipeConverter: call(input, annotation=NULL?, input_protein=?)
alt input_protein provided
FragPipeConverter->>OptionalProtein: read/use protein data
FragPipeConverter->>FragPipeConverter: merge PROTEIN into output
else no input_protein
FragPipeConverter->>FragPipeConverter: leave PROTEIN NULL or absent
end
FragPipeConverter->>Output: return msstats_data (PTM, PROTEIN?)
Output-->>User: msstats_data (PTM [, PROTEIN])
Estimated code review effort🎯 2 (Simple) | ⏱️ ~10 minutes Poem
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Actionable comments posted: 0
🧹 Nitpick comments (2)
vignettes/MSstatsPTM_LabelFree_Workflow.Rmd (1)
143-154: Add a file-existence guard for msstats_proteome_lf.csv to prevent vignette build failures.system.file returns "" if the resource is missing; fread("") will error during R CMD check. Guard it.
Apply this diff:
-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 +annot = data.table::fread(annot) +input_protein_path = system.file("tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv", + package = "MSstatsPTM") +if (!nzchar(input_protein_path) || !file.exists(input_protein_path)) { + stop("msstats_proteome_lf.csv not found in MSstatsPTM tinytest data") +} +input_protein = data.table::fread(input_protein_path) # Global profiling runR/converters.R (1)
244-265: Nice: LFQ example now shows input_protein; add a comment about the no-proteome fallback.Readers may not realize use_unmod_peptides is the fallback when no global run is available. Add a one-liner to the examples for discoverability.
Apply this diff:
#' 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") +#' # 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 = TRUE) #' head(msstats_data$PTM) #' head(msstats_data$PROTEIN)
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inst/tinytest/raw_data/Fragpipe/msstats_proteome_lf.csvis excluded by!**/*.csv
📒 Files selected for processing (4)
DESCRIPTION(1 hunks)R/converters.R(1 hunks)man/FragPipetoMSstatsPTMFormat.Rd(1 hunks)vignettes/MSstatsPTM_LabelFree_Workflow.Rmd(1 hunks)
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🔇 Additional comments (3)
man/FragPipetoMSstatsPTMFormat.Rd (1)
124-146: CSV packaged correctly — examples should find it.
msstats_proteome_lf.csv is present at inst/tinytest/raw_data/Fragpipe/msstats_proteome_lf.csv, so system.file(...) will locate it.vignettes/MSstatsPTM_LabelFree_Workflow.Rmd (1)
155-165: LFQ example CSV verified — headers present.msstats_proteome_lf.csv exists and contains the expected columns: ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, Condition, BioReplicate, Run, Intensity.
DESCRIPTION (1)
43-43: Approve — RoxygenNote bumped to 7.3.3; align CI/dev roxygen2DESCRIPTION (line 43) contains "RoxygenNote: 7.3.3". No functional change; ensure CI and developer environments use roxygen2 7.3.3 to avoid doc churn.
Motivation and Context
A user from this thread was not taking advantage of the converter enabling conversion of both the PTM and global profiling experiments together.
Changes
Testing
Vignettes and docs run fine
Checklist Before Requesting a Review
Summary by CodeRabbit
New Features
Documentation
Chores