print.createMetaData <- function(x,...){
drugvar <- x$auxiliary$passed.var$drugvar
namevar <- x$auxiliary$passed.var$namevar
correctionname <- x$auxiliary$passed.var$correctionname
meta <- x$meta.list$metadata.full
cat("Dose response experiment conducted on the drugs:\n")
cat(unique(meta[, drugvar]), "\n")
for(drug in unique(meta[, drugvar])){
cat("\n")
cat(length(unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)),
"cell lines have been exposed to", paste(drug, ":", sep = ""), "\n")
y <- unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)
y <- y[order(y)]
if(length(y) > 6){
cat(y[1:3], "...", y[(length(y)-3):length(y)], "\n")
}else{
cat(y, "\n")
}
}
cat("\n")
y <- unique(meta[meta[,namevar] == correctionname, drugvar])
if(length(y)==1){
cat("The following drug is associated with a drug color correction plate\n")
cat(y, "\n")
}
if(length(y)>1){
cat("The following drugs are associated with drug color correction plates\n")
cat(y, "\n")
}
if(length(y)==0){
cat("No drugs are associated with drug color correction plates\n")
}
cat("\n")
cat("Continue to function readDBFData. \n")
}
print.Absorbance <- function(x,...){
drugvar <- x$auxiliary$passed.var$drugvar
namevar <- x$auxiliary$passed.var$namevar
correctionname <- x$auxiliary$passed.var$correctionname
meta <- x$meta.list$metadata.full
cat("Dose response experiment conducted on the drugs:\n")
cat(unique(meta[, drugvar]), "\n")
for(drug in unique(meta[, drugvar])){
cat("\n")
cat(length(unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)),
"cell lines have been exposed to", paste(drug, ":", sep = ""), "\n")
y <- unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)
y <- y[order(y)]
if(length(y) > 6){
cat(y[1:3], "...", y[(length(y)-3):length(y)], "\n")
}else{
cat(y, "\n")
}
}
cat("\n")
cat("The molar masses of the drugs are:\n")
print(x$auxiliary$mol.data)
cat("If these are not correct you can change them using the function changeMolarMass")
cat("\n\n")
y <- unique(meta[meta[,namevar] == correctionname, drugvar])
if(length(y)==1){
cat("The following drug is associated with a drug color correction plate\n")
cat(y, "\n\n")
cat("Continue to function drugColorCorrection \n")
}
if(length(y)>1){
cat("The following drugs are associated with drug color correction plates\n")
cat(y, "\n\n")
cat("Continue to function drugColorCorrection \n")
}
if(length(y)==0){
cat("No drugs are associated with drug color correction plates\n\n")
cat("Continue to function bgModel to perform normalisation \n")
}
}
print.drugColorCorrection <- function(x,...){
drugvar <- x$auxiliary$passed.var$drugvar
namevar <- x$auxiliary$passed.var$namevar
correctionname <- x$auxiliary$passed.var$correctionname
meta <- x$meta.list$metadata.full
cat("Dose response experiment conducted on the drugs:\n")
cat(unique(meta[, drugvar]), "\n")
for(drug in unique(meta[, drugvar])){
cat("\n")
cat(length(unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)),
"cell lines have been exposed to", paste(drug, ":", sep = ""), "\n")
y <- unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)
y <- y[order(y)]
if(length(y) > 6){
cat(y[1:3], "...", y[(length(y)-3):length(y)], "\n")
}else{
cat(y, "\n")
}
}
cat("\n")
cat("Continue to function bgModel to perform normalisation \n")
}
print.bgModel <- function(x,...){
drugvar <- x$auxiliary$passed.var$drugvar
namevar <- x$auxiliary$passed.var$namevar
correctionname <- x$auxiliary$passed.var$correctionname
meta <- x$meta.list$metadata.full
cat("Dose response experiment conducted on the drugs:\n")
cat(unique(meta[, drugvar]), "\n")
for(drug in unique(meta[, drugvar])){
cat("\n")
cat(length(unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)),
"cell lines have been exposed to", paste(drug, ":", sep = ""), "\n")
y <- unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)
y <- y[order(y)]
if(length(y) > 6){
cat(y[1:3], "...", y[(length(y)-3):length(y)], "\n")
}else{
cat(y, "\n")
}
}
cat("\n")
cat("Continue to function bootstrap to simulate datasets used for confidence intervals \n")
}
print.bootstrap <- function(x,...){
drugvar <- x$auxiliary$passed.var$drugvar
namevar <- x$auxiliary$passed.var$namevar
correctionname <- x$auxiliary$passed.var$correctionname
meta <- x$meta.list$metadata.full
cat("Dose response experiment conducted on the drugs:\n")
cat(unique(meta[, drugvar]), "\n")
for(drug in unique(meta[, drugvar])){
cat("\n")
cat(length(unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)),
"cell lines have been exposed to", paste(drug, ":", sep = ""), "\n")
y <- unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)
y <- y[order(y)]
if(length(y) > 6){
cat(y[1:3], "...", y[(length(y)-3):length(y)], "\n")
}else{
cat(y, "\n")
}
}
cat("\n")
cat("Continue to function doseResponseModel to fit the dose response models. \n")
}
print.doseResponseModel <- function(x,...){
drugvar <- x$auxiliary$passed.var$drugvar
namevar <- x$auxiliary$passed.var$namevar
correctionname <- x$auxiliary$passed.var$correctionname
meta <- x$meta.list$metadata.full
cat("Dose response experiment conducted on the drugs:\n")
cat(unique(meta[, drugvar]), "\n")
for(drug in unique(meta[, drugvar])){
cat("\n")
cat(length(unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)),
"cell lines have been exposed to", paste(drug, ":", sep = ""), "\n")
y <- unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)
y <- y[order(y)]
if(length(y) > 6){
cat(y[1:3], "...", y[(length(y)-3):length(y)], "\n")
}else{
cat(y, "\n")
}
}
cat("\n")
#cat("Continue to function doseResponseModel to simulate datasets used for confidence intervals \n")
}
print.summary.DRdata <- function(x,...){
drugvar <- x$auxiliary$passed.var$drugvar
namevar <- x$auxiliary$passed.var$namevar
correctionname <- x$auxiliary$passed.var$correctionname
meta <- x$meta.list$metadata.full
cat("Dose response experiment conducted on the drugs:\n")
cat(unique(meta[, drugvar]), "\n")
for(drug in unique(meta[, drugvar])){
cat("\n")
cat(length(unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)),
"cell lines have been exposed to", paste(drug, ":", sep = ""), "\n")
y <- unique(meta[meta[, drugvar] == drug,namevar] %w/o% correctionname)
y <- y[order(y)]
if(length(y) > 6){
cat(y[1:3], "...", y[(length(y)-3):length(y)], "\n")
}else{
cat(y, "\n")
}
}
cat("\n")
#cat("Continue to function doseResponseModel to simulate datasets used for confidence intervals \n")
}
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