rplec (version 0.1.3)

plec: Estimate DNA-methylation-based gestational age

Description

This function estimate gestational age (GA) using BMIQ-normalized beta values. The estimated GA is a sum of normal and residual GAs. The latter is a sum of condition- and trimester-specific, residual GAs.

Usage

plec(norm_beta, type = "stack", verbose = FALSE)

Value

A data frame of the estimated GA.

Arguments

norm_beta

A data frame of normalized beta values where each column represents a sample and each row represent a probe. This data frame must be the output of bmiq_norm_450k function. The rows must be named according to the probe IDs. Meanwhile, the columns must be named according to the sample IDs.

type

An character indicating the type of outputs which are primarily: (1) "stack" (default) for the estimated GA; (2) "normal" for the estimated normal GA; (3) "residual" for the estimated residual GA; (4) "condition" for the condition-specific, estimated residual GA; and (5) "trimester" for the trimester-specific, estimated residual GA. In addition, a user can obtain the output of a single submodel using the column name (except predictor) in plec_int_coef. Use data(plec_int_coef) to load this data frame.

verbose

A logical scalar indicating whether to show a progress bar.

Examples

# \donttest{
  beta_values_case <- download_beta_values_case()
  norm_beta_values_case <- bmiq_norm_450k(beta_values_case)
  dnam_ga_case <- plec(norm_beta_values_case)
# }