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#' @rdname scramblase_assay_plot
#' @export
scramblase_assay_stats <- function(
x,
scale_to = c("model","data"),
ppr_scale_factor = 0.65,
force_through_origin = TRUE,
generation_of_algorithm = c(2, 1),
split_by_experiment = TRUE,
r_bar = 88,
sigma_r_bar = 28){
UseMethod("scramblase_assay_stats",x)
}
#' @export
scramblase_assay_stats.data.frame <- function(x, ...){
base_function_scramblase_assay_stats(x, ...)
}
#' @export
scramblase_assay_stats.character <- function(x, ...){
parsedInputFile <- read_scramblase_input_file(x)
withr::with_dir(
dirname(x),
base_function_scramblase_assay_stats(x = parsedInputFile, ...)
)
}
base_function_scramblase_assay_stats <- function(
x,
scale_to = c("model","data"),
ppr_scale_factor = 0.65,
force_through_origin = TRUE,
generation_of_algorithm = c(2, 1),
split_by_experiment = TRUE,
r_bar = 88,
sigma_r_bar = 28){
# Check Prerequisites -----------------------------------------------------
validatedParams <- scramblase_assay_input_validation(
x = x,
scale_to = scale_to,
ppr_scale_factor = ppr_scale_factor,
force_through_origin = force_through_origin,
generation_of_algorithm = generation_of_algorithm,
split_by_experiment = split_by_experiment,
r_bar = r_bar,
sigma_r_bar = sigma_r_bar)
x <- validatedParams[["x"]]
scale_to <- validatedParams[["scale_to"]]
ppr_scale_factor <- validatedParams[["ppr_scale_factor"]]
force_through_origin <- validatedParams[["force_through_origin"]]
generation_of_algorithm <- validatedParams[["generation_of_algorithm"]]
split_by_experiment <- validatedParams[["split_by_experiment"]]
r_bar <- validatedParams[["r_bar"]]
sigma_r_bar <- validatedParams[["sigma_r_bar"]]
# Processing --------------------------------------------------------------
processedListFromX <- scramblase_assay_calculations(
x = x,
scale_to = scale_to,
ppr_scale_factor = ppr_scale_factor,
force_through_origin = force_through_origin,
generation_of_algorithm = generation_of_algorithm,
split_by_experiment = split_by_experiment,
r_bar = r_bar,
sigma_r_bar = sigma_r_bar)
processedListFromX <- lapply(processedListFromX,function(y){y[["Raw"]]})
# Assemble the output -----------------------------------------
output <- plyr::rbind.fill(processedListFromX)
if (split_by_experiment) {
output <- output[!duplicated(output$CombinedId),]
} else {
output <- output[!duplicated(output$`Experimental Series`),]
}
if (split_by_experiment) {
columns <- c("Fit Constant (a)","Experimental Series","Experiment")
} else {
columns <- c("Fit Constant (a)","Experimental Series")
}
output <- output[which(names(output) %in% columns)]
output["Fit Constant (a)"] <- signif(output["Fit Constant (a)"], digits = generation_of_algorithm * 2)
names(output)[which(names(output) == "Fit Constant (a)")] <- "Fit Constant"
# Return ------------------------------------------------------------------
return(output)
}
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