regression_utility: regression_utility helper function

In rBiasCorrection: Correct Bias in DNA Methylation Analyses

regression_utility helper function

Description

Internal function to carry out the regression calculations.

Usage

regression_utility(
  data,
  samplelocusname,
  locus_id = NULL,
  rv,
  mode = NULL,
  logfilename,
  minmax,
  seed = 1234
)

Arguments

data	A data.table object that contains the calibration data.
samplelocusname	A character string. In type 1 data: locus name - name of the gene locus under investigation. In type 2 data: sample name - name of the sample under investigation.
locus_id	A character string. Default: NULL. ID of the respective locus (only used in type 2 correction).
rv	A list object. A list that contains additional objects needed for the algorithms.
mode	A character string. Default: NULL. Used to indicate "corrected" calibration data.
logfilename	A character string. Path to a file to save the log messages (default = paste0(tempdir(), "/log.txt")).
minmax	A logical, indicating which equations are used for BiasCorrection (default: FALSE). If TRUE, equations are used that include the respective minima and maxima of the provided data.
seed	A integer value. The seed used when solving the unknowns in the hyperbolic regression equation and the cubic regression equation. Important for reproducibility (default: 1234).

Value

The function performs the regression calculations and returns the results in a list.

Examples

# define list object to save all data
rv <- list()
rv$minmax <- TRUE
rv$selection_method <- "RelError"
rv$sample_locus_name <- "Test"
rv$seed <- 1234

# define logfilename
logfilename <- paste0(tempdir(), "/log.txt")

# import experimental file
exp_type_1 <- rBiasCorrection::example.data_experimental
rv$fileimport_experimental <- exp_type_1$dat

# import calibration file
cal_type_1 <- rBiasCorrection::example.data_calibration
rv$fileimport_calibration <- cal_type_1$dat
rv$vec_cal <- cal_type_1$vec_cal

# perform regression
regression_results <- regression_utility(
  rv$fileimport_calibration,
  "Testlocus",
  locus_id = NULL,
  rv = rv,
  mode = NULL,
  logfilename,
  minmax = rv$minmax,
  seed = rv$seed
)
length(regression_results)
class(regression_results)

rBiasCorrection documentation built on June 21, 2022, 1:05 a.m.