agep: Age Prediction from methylomic expression data

In schalkwyk/wateRmelon: Illumina DNA methylation array normalization and metrics

Age Prediction from methylomic expression data

Description

Predict age of samples using Horvaths Coefficients

Usage

agep(betas, coeff = NULL, method = c('horvath', 'hannum', 'phenoage', 'skinblood', 'lin', 'all'), n_missing = TRUE, missing_probes = FALSE, ...)

Arguments

betas	Matrix of betas or MethyLumiSet or MethylSet object.
coeff	If NULL, will default to whatever method is specified in method. If not NULL, the expected input should be a vector of coefficients and intercept
method	Currently: "horvath", "hannum", "phenoage", "skinblood", "lin" and "all", if "all" agep will seek to calculate ages using all methods else will use the method specified. Default is "horvath".
n_missing	Logical, additionally output the number of missing CpGs for each sample using the specified method or coeff list.
missing_probes	Logical, additionally output the names of missing CpGs for each sample using the specified method or coeff list.
...	To pass to arguments to downstream functions to specify adult.age

Value

Returns matrix of predicted ages per sample. With additional columns created whether n_missing or missing_probes are specified. If method is "all" then all ages will be provided in the same matrix output

Author(s)

Original Functions: Steve Horvath

wateRmelon Implementation: Tyler Gorrie-Stone, Leo Schalkwyk, Louis El Khoury

References

Horvath S: DNA methylation age of human tissues and cell types. Genome Biology 2013, 14:R115

Examples

data(melon)
agep(melon,coeff=NULL, method="all", n_missing=FALSE)
agep(melon,coeff=NULL, method="horvath", n_missing=TRUE)

schalkwyk/wateRmelon documentation built on Aug. 13, 2024, 9:52 a.m.