uplot_reproducibility: Check Reproducibility of Sample Analyses

In ume: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

Check Reproducibility of Sample Analyses

Description

Computes reproducibility of sample analyses based on the relative intensity column (norm_int). For each molecular formula (mf), the function calculates:

• number of occurrences (N)

• median relative intensity (ri)

• relative standard deviation (RSD = sd/median × 100)

It also bins ri into integer bins and calculates the median RSD per bin.

The function returns:

• processed tables

• two ggplot2 objects:

  • intensity vs RSD scatter plot

  • binned median RSD plot

Usage

uplot_reproducibility(df, ri = "norm_int")

Arguments

df	A data.table or data.frame containing at least columns mf and the intensity column defined in ri.
ri	Character string: name of the intensity column. Default: "norm_int".

Value

A list containing:

tmp

Summary table by molecular formula

tmp2

Binned median RSD table

plot_rsd

Scatter plot of RI vs RSD (ggplot2)

plot_bins

Median RSD per bin (ggplot2)

See Also

Other plots: uplot_cluster(), uplot_cvm(), uplot_dbe_minus_o_freq(), uplot_dbe_vs_c(), uplot_freq_ma(), uplot_freq_vs_ppm(), uplot_hc_vs_m(), uplot_heteroatoms(), uplot_isotope_precision(), uplot_kmd(), uplot_lcms(), uplot_ma_vs_mz(), uplot_ms(), uplot_n_mf_per_sample(), uplot_pca(), uplot_ratios(), uplot_ri_vs_sample(), uplot_vk()

Examples

out <- uplot_reproducibility(mf_data_demo, ri = "norm_int")
out$plot_rsd
out$plot_bins

ume documentation built on Dec. 13, 2025, 1:06 a.m.