docs(Philosopher): Add examples for using Philosopher/Fragpipe converter#90
docs(Philosopher): Add examples for using Philosopher/Fragpipe converter#90tonywu1999 merged 3 commits intodevelfrom
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WalkthroughThe changes focus on improving documentation and testing for the Changes
Estimated code review effort🎯 2 (Simple) | ⏱️ ~7 minutes Poem
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🧹 Nitpick comments (1)
man/PhilosophertoMSstatsTMTFormat.Rd (1)
78-88: Consider wrapping the example in\\donttest{}to keep CRAN checks fast.Reading two files with
fread()and running the full converter is fine for users, but CRAN requires that examples run in < ~5 s on slow hardware. Wrapping the whole block in\donttest{}(or\dontrun{}if runtime is unpredictable) prevents timeouts while still rendering the code for users.-\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) - -} +\examples{ +\donttest{ +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) +} +}
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⛔ Files ignored due to path filters (3)
inst/.DS_Storeis excluded by!**/.DS_Storeinst/raw_data/Philosopher/MSstatsTMT_annotation.csvis excluded by!**/*.csvinst/raw_data/Philosopher/msstats.csvis excluded by!**/*.csv
📒 Files selected for processing (6)
DESCRIPTION(1 hunks)R/converters.R(1 hunks)R/utils_MSstatsTMT.R(1 hunks)man/MSstatsTMT.Rd(1 hunks)man/PhilosophertoMSstatsTMTFormat.Rd(1 hunks)tests/testthat/test-converters.R(1 hunks)
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🔇 Additional comments (7)
R/utils_MSstatsTMT.R (1)
17-18: LGTM! Modern roxygen2 package documentation.The update from
@docType packageandNULLto@keywords internaland"_PACKAGE"follows current roxygen2 best practices for package-level documentation. This modernizes the documentation structure without affecting functionality.man/MSstatsTMT.Rd (2)
40-41: LGTM! Author list updated.The addition of Tony Wu and Deril Raju to the author list is appropriate and maintains proper attribution.
47-47: LGTM! Documentation consistency maintained.The addition of the
internalkeyword aligns with the corresponding changes inR/utils_MSstatsTMT.R, maintaining consistency across the package documentation.R/converters.R (1)
335-344: Excellent example documentation!The added example code demonstrates proper usage of the
PhilosophertoMSstatsTMTFormatfunction with realistic data loading usingsystem.file()anddata.table::fread(). This follows the established pattern from other converter functions and provides users with a clear, executable example.DESCRIPTION (1)
26-26: LGTM! Routine roxygen2 version update.The update from RoxygenNote 7.3.1 to 7.3.2 is a standard maintenance task that aligns with the documentation improvements throughout the package.
tests/testthat/test-converters.R (1)
30-41: Excellent test coverage addition!The new test case for
PhilosophertoMSstatsTMTFormatfollows good testing practices by:
- Loading realistic test data using the same approach as the documentation example
- Verifying the function executes successfully
- Asserting a specific expected outcome (550 rows)
- Following the established testing pattern in the file
This provides valuable regression protection for the converter function.
man/PhilosophertoMSstatsTMTFormat.Rd (1)
80-84: Verify that the example data files are installed with the package.
system.file("raw_data/Philosopher/…", package = "MSstatsTMT")will return an empty string if those paths are not included underinst/at build time, causing the example (and the new test) to fail. Double-check that:
inst/raw_data/Philosopher/msstats.csvinst/raw_data/Philosopher/MSstatsTMT_annotation.csvare present and listed in
R/’s@examplefiles section or ininst/extdata, and that they are ≤ 5 MB to satisfy CRAN size limits.
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