Package: sfi 1.0.0

Miao YU

sfi: Data analysis for Single File Injections (SFIs) mode LC-MS analysis

Data analysis for Single File Injections(SFIs) mode LC-MS analysis. In SFIs mode, pooled samples are initially injected to serve as reference peaks for subsequent analyses. Repeated injections of individual samples are then performed at fixed time intervals using isocratic elution. This package provides the functions to analyze data from SFIs mode including peak picking and peak reassignment.

Authors:Miao YU [aut, cre]

sfi_1.0.0.tar.gz
sfi_1.0.0.zip(r-4.7)sfi_1.0.0.zip(r-4.6)sfi_1.0.0.zip(r-4.5)
sfi_1.0.0.tgz(r-4.6-x86_64)sfi_1.0.0.tgz(r-4.6-arm64)sfi_1.0.0.tgz(r-4.5-x86_64)sfi_1.0.0.tgz(r-4.5-arm64)
sfi_1.0.0.tar.gz(r-4.7-arm64)sfi_1.0.0.tar.gz(r-4.7-x86_64)sfi_1.0.0.tar.gz(r-4.6-arm64)sfi_1.0.0.tar.gz(r-4.6-x86_64)
sfi_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
sfi/json (API)
NEWS

# Install 'sfi' in R:

install.packages('sfi', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yufree/sfi/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

sfi - Demo sfi data

On BioConductor:sfi-1.1.0(bioc 3.24)sfi-1.0.0(bioc 3.23)

massspectrometry metabolomics featureextraction cpp

4.74 score 1 stars 201 downloads 10 exports 106 dependencies

Last updated from:8292496bd7 (on RELEASE_3_23). Checks:1 NOTE, 13 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	247
linux-devel-arm64	OK	330
linux-devel-x86_64	OK	349
source / vignettes	OK	322
linux-release-arm64	OK	333
linux-release-x86_64	OK	374
macos-release-arm64	OK	295
macos-release-x86_64	OK	419
macos-oldrel-arm64	OK	164
macos-oldrel-x86_64	OK	570
windows-devel	OK	283
windows-release	OK	292
windows-oldrel	OK	278
wasm-release	OK	198

Exports:find_2d_peaks find_peaks_low_res get_qc_features get_sfi_params getidelta getmzml getsff getsfm getwindow run_app

Dependencies:abind animation askpass base64enc BH Biobase BiocGenerics biocmake BiocParallel bslib cachem cli codetools cpp11 crosstalk curl data.table DelayedArray digest dir.expiry dplyr enviGCMS evaluate farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite kernlab knitr labeling lambda.r later lattice lazyeval lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mime mixtools mzR ncdf4 nlme openssl otel pillar pkgconfig plotly promises ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp Rdisop Rhdf5lib rlang rmarkdown S4Arrays S4Vectors S7 sass scales segmented Seqinfo snow SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XVector yaml

sfi workflow

Rendered fromworkflow.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-18
Started: 2025-05-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Feature extraction core function	find_2d_peaks
Find peaks in low-resolution data using the 2D peak finding algorithm	find_peaks_low_res
Generate Quality Control Feature List	get_qc_features get_qc_features.default get_qc_features.sfi_peaks
Quality Control for Mass Spectrometry Data	get_sfi_params get_sfi_params.default get_sfi_params.sfi_peaks
Optimize Delta Retention Time	getidelta getidelta.default getidelta.sfi_peaks
Read mzML File and Extract m/z, Retention Time, and Intensity	getmzml
Cluster and Pair m/z and Retention Time Features	getsff getsff.default getsff.sfi_peaks
Generate Sample Feature Matrix (SFM)	getsfm getsfm.default getsfm.sfi_peaks
Determine Optimal Retention Time Window	getwindow getwindow.default getwindow.sfi_peaks
Run sfi Shiny App	run_app
Demo sfi data	sfi