impute_AAT: Impute Alpha-1 antitrypsin (AAT)

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

Description

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

Usage

impute_AAT(GlycA, FAw3, VLDL.D, HDL3.C, LDL.D, Phe, Leu, ApoB, Alb, Tyr, bOHBut,
  BMI, Ala, L.HDL.TG, Ile, Ace, His, HDL.TG, 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.
FAw3	NMR measurement for Omega-3 fatty acids. Measurements should be between 0.196–1.18 mmol/L.
VLDL.D	NMR measurement for the mean diameter of VLDL particles. Measurements should be between 33–41 nm.
HDL3.C	NMR measurement for cholesterol in the HDL-3 fraction. Measurements should be between 0.421–0.647 mmol/L.
LDL.D	NMR measurement for the mean diameter of LDL particles. Measurements should be between 23.2–24.1 nm.
Phe	NMR measurement for phenylalanine. Measurements should be between 0.0555–0.118 mmol/L.
Leu	NMR measurement for leucine. Measurements should be between 0.0295–0.138 mmol/L.
ApoB	NMR measurement for Apolipoprotein B. Measurements should be between 0.365–1.48 g/L.
Alb	NMR measurement for albumin. Measurements should have a signal area ranging between 0.0733–0.101.
Tyr	NMR measurement for tyrosine. Measurements should be between 0.0279–0.124 mmol/L.
bOHBut	NMR measurement for 3-hydroxybutyrate. Measurements should be between 0.0331–0.872 mmol/L.
BMI	Body Mass Index. Measurements should be between 16.17–47.44 kg/m^2.
Ala	NMR measurement for alanine. Measurements should be between 0.274–0.557 mmol/L.
L.HDL.TG	NMR measurement for triglycerides within large HDL particles. Measurements should be between 0.000462–0.0933 mmol/L.
Ile	NMR measurement for isoleucine. Measurements should be between 0.024–0.103 mmol/L.
Ace	NMR measurement for acetate. Measurements should be between 0.029–1.32 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.
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 AAT measurements ranging between 0.64–2.58 mg/L or measurements standardised to the population if standardised = 'TRUE'.

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