plec {rplec} | R Documentation |
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)
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 |
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 |
verbose |
A logical scalar indicating whether to show a progress bar. |
Value
A data frame of the estimated GA.
Examples
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)