📝 CodeRabbit Chat: Fix Spectronaut CSV column selection for Datasets API - #20
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R/clean_spectronaut.R:9-12: added block_size parameter (default 16L * 1024L * 1024L) with coerce + validation. R/clean_spectronaut.R:44: CsvReadOptions$create now uses the parameter. R/converters.R:120-125: new @param block_size roxygen with the straddling-object workaround note. R/converters.R:148-156: bigSpectronauttoMSstatsFormat gains block_size, plumbed to reduceBigSpectronaut. tests/testthat/test-converters.R:97-163: validation tests (rejects negative/zero/NA/vector/string) + plumbing tests (default forwards 16 MiB, override forwards user's value). man/bigSpectronauttoMSstatsFormat.Rd: regenerated from roxygen.
…setnames so the package is data.table-aware (cedta()). R/clean_spectronaut.R:103-187: rewrote cleanSpectronautChunk in data.table: setDT(input) at entry; subsequent operations modify in place via :=. Two-step rename (setnames for standardize, then setnames with skip_absent = TRUE to map standardized→MSstats) matches the MSstatsConvert family pattern. Conditional NA assignment uses mask form dt[cond, Intensity := NA_real_]. Q-value filters preserve dplyr::if_else NA semantics via explicit is.na(EGQvalue) | EGQvalue >= cutoff. Dropped the leftover dplyr::collect(head(dplyr::select(...))) pattern — was a no-op residue from a prior refactor. Function shrank from ~88 lines to ~64. DESCRIPTION:20: added data.table to Imports. NAMESPACE: regenerated, now imports :=, .SD, setDT, setnames from data.table. tests/testthat/test-converters.R:97-211: 5 new tests — schema smoke test, filter_by_excluded, filter_by_identified, filter_by_qvalue (covering the NA-q-value case), and FFrgLossType row drop.
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tonywu1999
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Code changes was requested by @Rudhik1904.
The following files were modified:
R/clean_spectronaut.R