qc {rplec} | R Documentation |
Perform quality control
Description
This function evaluates the precision of DNA-methylation-based (DNAm) gestational age (GA) based on calibration, root mean square error (RMSE), mean absolute error (MAE), and Pearson's correlation coefficient (r). The sample identifiers (IDs) are automatically matched among the DNAm-GA, GA, and phenotype (optional). Only GA from 5 to 44 weeks' gestation are shown in the calibration plot.
Usage
qc(dnam_ga, ga, phenotype = NULL)
Arguments
dnam_ga |
A data frame of DNA-methylation-based GA. This data frame
must be the output of |
ga |
A data frame of GA. There is only one column, i.e., |
phenotype |
A data frame of phenotype (optional). There is only one
column, i.e., |
Value
A ggplot object of calibration plot with RMSE, MAE, and r.
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)
data(ga)
ga_case <- ga[phenotype$phenotype == "Case", , drop = FALSE]
set.seed(1)
qc(dnam_ga_case, ga_case)