humanlipidome: Concentrations of lipids in a human plasma reference sample

In tommi-s/lipidomeR: Integrative Visualizations of the Lipidome

Description

This data set contains concentrations of 403 named lipids in human plasma standard reference material (SRM 1950).

Usage

data( humanlipidome )

Format

A data frame with 403 rows and 2 variables:

Name

Name of the lipid

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"
)

tommi-s/lipidomeR documentation built on March 17, 2020, 12:14 a.m.