NEWS

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sfi 0.99.5

• vignette updates
• trigger build

sfi 0.99.4

• getsfm() now returns a SummarizedExperiment object instead of a data.frame, with intensities in the assay slot and feature metadata in rowData.
• Expanded vignette with "Using the Results" and "Downstream Analysis" sections, demonstrating the SummarizedExperiment output.
• Added SummarizedExperiment, S4Vectors, and methods to Imports.
• Updated Shiny app and documentation to handle SummarizedExperiment from getsfm().

sfi 0.99.3

• Renamed getqc() to get_sfi_params() to better reflect its purpose. It now returns a named vector c(window, idelta) instead of an unnamed vector.
• Renamed getqcdf() to get_qc_features() for clarity.
• getmzml() now returns a data.frame with named columns (mz, intensity, rt) instead of a matrix.
• get_qc_features() now sets informative row names corresponding to the sample injection index.
• Detailed documentation for return values and column definitions for getsff, and get_qc_features.
• Updated README installation instructions for Bioconductor.
• Added a comprehensive testthat test suite.
• Updated DESCRIPTION to set LazyData: false per Bioconductor guidelines.
• Updated find_2d_peaks to return an object with class c("sfi_peaks", "data.frame"). All the related functions have been updated.

sfi 0.99.2

• Recover demo data with new algorithm for getsff
• Add find_peaks_low_res() function for low-resolution (unit mass) data analysis
• Add run_app() function to launch Shiny app for SFI data analysis
• Add interactive Shiny app with GUI for feature extraction and alignment
• Update NAMESPACE to export new functions and import required dependencies
• Add documentation for new functions and updated existing functions
• Add shiny and DT packages to Imports for interactive functionality

sfi 0.99.1

• Fix warning for C++ code
• Remove sfi.Rproj from git
• Change demo data with smaller size

sfi 0.99.0

• Initial BioC submission.