R data frame aggregation

R Data Frame Aggregation

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Summary

Consolidate programmatically extracted spectral attributes from individual scans into a single tabular data frame using R subsetting operators and iteration. This is essential for transforming per-scan raw instrument data into analysis-ready tabular formats suitable for downstream statistical and visualization workflows.

When to use

When you have extracted multiple spectral attributes (e.g., base-peak m/z, intensity, retention time, scan index) from individual MS scans via accessor functions and need to organize them into a single rectangular data frame for batch analysis, filtering, or export to external tools.

When NOT to use

• Input data is already a feature matrix or aggregated table—skip to statistical analysis or visualization.
• You need to preserve all m/z–intensity pairs for each spectrum, not just base-peak values; use alternative export formats (mzML) or in-memory list structures instead.
• Raw file is in an exchange format (mzML, mzXML) already—use format-specific parsers (mzR, proteowizardR) rather than rawrr.

Inputs

• rawrrSpectrum objects (extracted via readSpectrum)
• scan index data frame (from readIndex)
• filtered scan numbers (integer vector)

Outputs

• data frame with columns for scan index and spectral attributes (e.g., base_peak_mz, base_peak_intensity)

How to apply

Iterate through a filtered scan index (e.g., MS1-level scans obtained via readIndex() and subset on ms_level==1), calling readSpectrum() on each scan number to extract the spectrum object. Use R's subsetting operators ($, [[) to programmatically extract target attributes (base-peak m/z, intensity, scan number) from each rawrrSpectrum object. Aggregate these pairs into vectors or lists, then bind them into a data frame using data.frame() or cbind(). Verify correctness by checking row count matches scan count, column names are meaningful, and data types are appropriate (numeric for m/z/intensity, integer for scan indices).

Related tools

• rawrr (Provides readSpectrum(), readIndex(), and accessor functions to extract spectral data from Thermo .raw files and return rawrrSpectrum objects amenable to subsetting) — https://github.com/fgcz/rawrr
• RawFileReader (Underlying .NET assembly wrapped by rawrr; implements the binary file I/O and spectral data extraction) — https://github.com/thermofisherlsms/RawFileReader
• Spectra (Alternative downstream consumer of aggregated MS data; MsBackendRawFileReader integrates rawrr data into Spectra package workflows) — https://bioconductor.org/packages/Spectra

Examples

# Install rawrr and load raw file
rawrr::installRawrrExe()
H <- rawrr::readFileHeader('20181113_010_autoQC01.raw')
idx <- rawrr::readIndex('20181113_010_autoQC01.raw')
idx_ms1 <- subset(idx, idx$ms_level == 1)
df <- data.frame(scan = idx_ms1$scan, base_peak_mz = NA, base_peak_intensity = NA)
for (i in seq_along(idx_ms1$scan)) {
  spec <- rawrr::readSpectrum('20181113_010_autoQC01.raw', idx_ms1$scan[i])
  df$base_peak_mz[i] <- spec$mz[which.max(spec$intensity)]
  df$base_peak_intensity[i] <- max(spec$intensity)
}

Evaluation signals

• Row count in output data frame equals the number of filtered scans (e.g., if 10,000 MS1 scans were selected, result should have 10,000 rows).
• All expected columns are present and named correctly (e.g., 'scan_index', 'base_peak_mz', 'base_peak_intensity').
• No NA or NaN values in key columns unless explicitly expected (e.g., scans with no peaks).
• m/z values are numeric, within instrument's expected mass range (e.g., 50–2000 m/z for typical Orbitrap), and base-peak m/z is the position of maximum intensity within each spectrum.
• Data frame can be successfully written to CSV or loaded into downstream analysis tools (ggplot2, statistical functions) without type conversion errors.

Limitations

• rawrr requires installation of the compiled RawFileReader executable via rawrr::installRawrrExe(); not all platforms may have stable releases.
• Accessor operators ($, [[]]) on rawrrSpectrum objects are not well-documented; users must rely on package vignettes and examples.
• Iterative extraction via readSpectrum() called per scan is slower than bulk operations; for large datasets (>100,000 scans), performance may be limiting.
• Aggregation into a single data frame assumes all scans contain the same attributes; heterogeneous scan types (MS1 vs MS2 with different metadata) may require pre-filtering or list-of-data-frames structures.
• The article focuses on base-peak extraction; full spectral profiles (all m/z–intensity pairs) require alternative strategies beyond simple data-frame aggregation.

Evidence

• [other] Iterate through filtered scans and call readSpectrum() on each scan number to extract spectral data: "Iterate through filtered scans and call readSpectrum() on each scan number to extract spectral data. For each spectrum, extract the base-peak m/z and its corresponding intensity."
• [other] rawrr provides accessor functions and subsetting operators to programmatically extract spectral attributes: "rawrr provides accessor functions and subsetting operators ($, [[) to programmatically extract spectral attributes from rawrrSpectrum objects"
• [other] Aggregate extracted m/z and intensity pairs into a data frame: "Aggregate extracted m/z and intensity pairs into a data frame with scan index and base-peak columns."
• [methods] R functions request access to data via C# wrapper methods; extracted information is written to temporary location, read back into memory and parsed into R objects: "R functions requesting access to data stored in binary raw files invoke compiled C# wrapper methods using a system call. In order to return extracted data back to the R layer we use file I/O. More"
• [other] Generate scan index using readIndex() to retrieve all scans; filter to retain only MS1-level scans: "Generate a scan index using readIndex() to retrieve all scans. Filter the index to retain only MS1-level scans by subsetting on ms_level==1."