impute_AGP: Impute Alpha-1-acid glcyoprotein (AGP)

In InouyeLab/imputegp: Impute GlycA glycoproteins from serum NMR data in population studies

Description

Imputes the concentrations of AGP from serum NMR measurements in healthy population-based samples.

Usage

impute_AGP(GlycA, TotFA, IDL.FC, L.HDL.FC, His, HDL.TG, BMI, S.HDL.FC, S.LDL.TG,
  bOHBut, LA, S.HDL.CE, Lac, S.VLDL.TG, Ace, Cit, SFA, Ala, XXL.VLDL.CE, Glol,
  Age, Crea, Gly, range_check = TRUE, standardised = FALSE,
  na.omit = TRUE)

Arguments

GlycA	NMR measurement for glycoprotein acetyls. Measurements should be between 0.869–2.24 mmol/L.
TotFA	NMR measurement for total fatty acids. Measurements should be between 5.58–17.1 mmol/L
IDL.FC	NMR measurement for free cholesterol within IDL particles. Measurements should be between 0.0515–0.368 mmol/L.
L.HDL.FC	NMR measurement for free cholesterol within large HDL particles. Measurements should be between 0.00134–0.208 mmol/L.
His	NMR measurement for histidine. Measurements should be between 0.0446–0.0913 mmol/L.
HDL.TG	NMR measurement for triglycerides within all HDL particles. Measurements should be between 0.0698–0.315 mmol/L.
BMI	Body Mass Index. Measurements should be between 16.17–47.44 kg/m^2.
S.HDL.FC	NMR measurement for free cholesterol within small HDL particles. Measurements should be between 0.0674–0.168 mmol/L.
S.LDL.TG	NMR measurement for triglycerides within small LDL particles. Measurements should be between 0.00478–0.076 mmol/L.
bOHBut	NMR measurement for 3-hydroxybutyrate. Measurements should be between 0.0331–0.872 mmol/L.
LA	NMR measurement for 18:2 linoleic acid. Measurements should be between 0.449–5.15 mmol/L.
S.HDL.CE	NMR measurement for cholesterol esters in small HDL particles. Measurements should be between 0.061–0.466 mmol/L.
Lac	NMR measurement for lactate. Measurements should be between 0.69–4.93 mmol/L.
S.VLDL.TG	NMR measurement for triglycerides within small VLDL particles. Measurements should be between 0.0135–0.76 mmol/L.
Ace	NMR measurement for acetate. Measurements should be between 0.029–1.32 mmol/L.
Cit	NMR measurement for citrate. Measurements should be between 0.0739–0.186 mmol/L.
SFA	NMR measurement for saturated fatty acids. Measurements should be between 2.07–7.02 mmol/L.
Ala	NMR measurement for alanine. Measurements should be between 0.274–0.557 mmol/L.
XXL.VLDL.CE	NMR measurement for cholesterol esters within extremely large VLDL particles. Measurements should be between 0.000000133–0.0169 mmol/L.
Glol	NMR measurement for glycerol. Measurements should be between 0.0415–0.312 mmol/L.
Age	The study participant's age in years. Measurements should be between 25–74 years old.
Crea	NMR measurement for creatinine. Measurements should be between 0.0182–0.347 mmol/L.
Gly	NMR measurement for glycine. Measurements should be between 0.182–0.632 mmol/L.
range_check	logical; if TRUE discard measurements that are not in the accepted range of values (see Details). If FALSE, no checking of input measurements or predicted concentrations will be performed.
standardised	logical; have measurements been standardised (i.e. using the scale function.)
na.omit	logical; should samples with missing values be omited? If FALSE missing values are set to the measurement's median in the model training dataset. Alternatively consider imputing missing values using impute.knn.

Details

The imputation models will only return a concentration where no input measurements were missing, and where all input measurements were within their acceptable predefined range of values. These correspond to their range of values in the training dataset. Similarly, the imputed measurement will be set to missing if the imputation model returns a concentration outside the range of values that were found in the training dataset.

Standardised measurements may also be used by setting standardised = 'TRUE', which is useful for cases where measurements must be adjusted for technical effects. In this case, all NMR measurements and BMI should be log transformed before scaling. Age and sex must also be standardised.

Value

A vector of AGP measurements ranging between 362–1,880 mg/L or measurements standardised to the population if standardised = 'TRUE'.

InouyeLab/imputegp documentation built on May 23, 2019, 7:17 a.m.