humanlipidome {lipidomeR}

Concentrations of lipids in a human plasma reference sample

Description

This data set contains concentrations of 403 named lipids in the 'National Institute of Standards and Technology Human Plasma Standard Reference Material' (NIST SRM 1950).

Usage

data( humanlipidome )

Format

A data frame with 403 rows and 2 variables:

Name

Name of the lipid. The names are in the format 'XY(C:D)', where 'XY' is the abbreviation of the lipid class, 'C' is the total number of carbon atoms in the fatty-acid chains, and 'D' is the total number of double-bonds in the fatty acid chains.

Concentration

Concentration of the lipid (umol/mL)

Source

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the 'Metabolomics Workbench', https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000004. The data can be accessed directly via its Project DOI: 10.21228/M8MW26. This work was supported by NIH grant, U2C- DK119886.

References

Quehenberger, O. et al. Lipidomics reveals a remarkable diversity of lipids in human plasma. J Lipid Res. 51, 3299-3305 (2010) (doi: 10.1194/jlr.M009449)

Examples

# Load the data set.
data( humanlipidome )
# Transform the concentrations into log-10 scale.
humanlipidome$"Concentration_log10_umol_per_mL" <-
   log10( humanlipidome$"Concentration" )
# Enumerate the lipid names into values.
names.mapping <- map_lipid_names( x = humanlipidome$"Name" )
# Create the lipidomeR heatmap of lipid concentrations.
heatmap_lipidome(
   x = humanlipidome[ , c( "Name", "Concentration_log10_umol_per_mL" ) ],
   names.mapping = names.mapping,
   class.facet = "wrap",
   x.names = "Name",
   fill.limits =
       range(
           x = humanlipidome$"Concentration_log10_umol_per_mL",
           na.rm = TRUE
       ),
   fill.midpoint =
       sum(
           range(
               x = humanlipidome$"Concentration_log10_umol_per_mL",
               na.rm = TRUE
           )
       ) / 2,
   melt.value.name = "Concentration_umol_per_mL_log10",
   scales = "free"
)