callingWaterfall: Drug sensitivity calling using waterfall plots
In CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages

Description Usage Arguments Details Value Examples

1. Sensitivity calls were made using one of IC50, ActArea or Amax

callingWaterfall(
  x,
  type = c("IC50", "AUC", "AMAX"),
  intermediate.fold = c(4, 1.2, 1.2),
  cor.min.linear = 0.95,
  name = "Drug",
  plot = FALSE
)

`x`	What type of object does this take in?
`type`	ic50: IC50 values in micro molar (positive values) actarea: Activity Area, that is area under the drug activity curve (positive values) amax: Activity at max concentration (positive values)
`intermediate.fold`	vector of fold changes used to define the intermediate sensitivities for ic50, actarea and amax respectively
`cor.min.linear`	`numeric` The minimum linear correlation to require?
`name`	`character` The name of the output to use in plot
`plot`	`boolean` Whether to plot the results

2. Sort log IC50s (or ActArea or Amax) of the cell lines to generate a <e2><80><9c>waterfall distribution<e2><80><9d>

3. Identify cutoff:

3.1 If the waterfall distribution is non-linear (pearson cc to the linear fit <=0.95), estimate the major inflection point of the log IC50 curve as the point on the curve with the maximal distance to a line drawn between the start and end points of the distribution.

3.2 If the waterfall distribution appears linear (pearson cc to the linear fit > 0.95), then use the median IC50 instead.

4. Cell lines within a 4-fold IC50 (or within a 1.2-fold ActArea or 20 difference) difference centered around this inflection point are classified as being <e2><80><9c>intermediate<e2><80><9d>, cell lines with lower IC50s (or ActArea/Amax values) than this range are defined as sensitive, and those with IC50s (or ActArea/Amax) higher than this range are called <e2><80><9c>insensitive<e2><80><9d>.

5. Require at least x sensitive and x insensitive cell lines after applying these criteria (x=5 in our case).

factor Containing the drug sensitivity status of each cellline.