msquant: Example mass spectrometry dataset.

In KechrisLab/MSPrep: Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data

Description

Data contains LC-MS samples for 2 subjects, each run with several different study design settings: spike-in (1x, 2x, 4x), batch (01, 02, 03), and technical replicate (A, B, C). The first two columns indicate mass-to-charge ratio and retention-time for the 2644 unique metabolites observed in the samples. The remaining 54 columns indicate metabolite abundance for each subject/spike-in/ batch/replicate combination.

Usage

data(msquant)

Format

Data frame containing 2644 observations of 56 samples

mz

Mass-to-charge ratio

rt

Retention-time

Neutral_Operator_Dif_Pos_1x_O1_A_01

The remaining columns specify metabolite abundances found in each subject/spike-in/batch/replicate combination. Each columns begins with 'Neutral_Operator_Dif_Pos' followed by the spike-in (1x, 2x, or 4x), then the batch (01, 02, or 03), the replicate (A, B, or C), and finally the subject ID (01 or 02), each seperated by '_'.

References

Hughes, G., Cruickshank-Quinn, C., Reisdorph, R., Lutz, S., Petrache, I., Reisdorph, N., … Kechris, K. (2014). MSPrep–summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data. Bioinformatics (Oxford, England), 30(1), 133–134. doi:10.1093/bioinformatics/btt589

Examples

  data(msquant)

KechrisLab/MSPrep documentation built on Feb. 2, 2022, 2:43 a.m.