predictEthnicity: Predicts ethnicity using placental DNA methylation microarray...

In wvictor14/planet: Placental DNA methylation analysis tools

Predicts ethnicity using placental DNA methylation microarray data

Description

Uses 1860 CpGs to predict self-reported ethnicity on placental microarray data.

Usage

predictEthnicity(betas, threshold = 0.75, force = FALSE)

Arguments

betas	n x m dataframe of methylation values on the beta scale (0, 1), where the variables are arranged in rows, and samples in columns. Should contain all 1860 predictors and be normalized with NOOB and BMIQ.
threshold	A probability threshold ranging from (0, 1) to call samples 'ambiguous'. Defaults to 0.75.
force	run even if missing predictors. Default is FALSE.

Details

Predicts self-reported ethnicity from 3 classes: Africans, Asians, and Caucasians, using placental DNA methylation data measured on the Infinium 450k/EPIC methylation array. Will return membership probabilities that often reflect genetic ancestry composition.

The input data should contain all 1860 predictors (cpgs) of the final GLMNET model.

It's recommended to use the same normalization methods used on the training data: NOOB and BMIQ.

Value

a tibble

Examples

## To predict ethnicity on 450k/850k samples

# Load placenta DNAm data
data(plBetas)
predictEthnicity(plBetas)

wvictor14/planet documentation built on June 18, 2024, 2:50 p.m.