sampledata: Simulated Metabolomics Data

In MetProc: Separate Metabolites into Likely Measurement Artifacts and True Metabolites

Description

This is a simulated dataset to show the format of the metabolomics data; patterns of missing data are generated roughly from a real metabolomics experiment. Rows represent metabolites and columns represent samples. The file contains 100 metabolites (rows) and 505 samples (480 biological sample columns and 25 pooled plasma columns) sorted by injection order. There are 20 biological samples between pooled plasma runs. Pooled plasma columns have prefix ‘PPP’ and biological samples are simple integers with no prefix.

Usage

sampledata

Format

The first row (Date) contains the date of processing. The second row (Inject) contains the injection number and is ordered from 1 to 505. The third row contains the column headers:

Metab is the metabolite ID.
Meth is the type of metabolite.
HMDB is the HMDB ID of the metabolite, if it exists.
m/z is the mass-to-charge ratio of the metabolite.
rt is the retention time.
Com contains any comments.
ProcID is the processing ID of the metabolite.

The remaining columns are either pooled plasma samples (prefix: ‘PPP’) or biological samples (prefix: No prefix). The basic structure of the csv file is as follows:

						Date	415	415	..	415	415	415	..
						Inject	1	2	..	21	22	23	..
Metab	Meth	HMDB	m/z	rt	Com	ProcID	PPP1	1	..	20	PPP2	21	..
M1	Lipid	H1	304	8.7		1	6.7	6.7	..	5.0	6.7	4.6	..
M2	Lipid	H2	309	7.6		2	1.0	1.1	..	1.1	1.0	1.2	..
..	..	..	..	..	..	..	..	..	..	..	..	..	..
M100	Lipid	H100	249	6.2		100	2.4	1.9	..	2.2	2.4	1.6	..

See Also

See read.met for example of reading this csv file for use.
See MetProc-package for examples of running the full process.

MetProc documentation built on May 2, 2019, 2:42 a.m.