| humanlipidome | R Documentation |
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).
data( humanlipidome )
A data frame with 403 rows and 2 variables:
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 of the lipid (umol/mL)
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.
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)
# 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"
)