compute_BMD_IC50: This function identify the BMD area and the IC50 value in the...

In angy89/TinderMIX: TinderMIX: An R package to cluster gene expression by contour plots

Usage

compute_BMD_IC50(immy, coord, geneName, activity_threshold = 0.1,
  BMD_response_threshold = 0.95, nDoseInt = 3, nTimeInt = 3,
  doseLabels = c("Late", "Middle", "Early"),
  timeLabels = c("Sensitive", "Intermediate", "Resilient"),
  toPlot = TRUE, addLegend = TRUE, tosave = FALSE, path = ".",
  mode = "cumulative")

Arguments

immy	z-maps of the fitted 3D model, with doses on the columns and time points on the rows
coord	matrix with x and y coordinate. The first column contain the doses, while the second one the time points
geneName	is a character string containing the gene name
activity_threshold	threshold defining the responsive gene area. Eg. if the immy maps contains genes logFC, then an activity_threhdold = 0.58 means that the active area will be the one with an effect of 1.5 bigger or smaller than the controls
BMD_response_threshold	a threshold to define the portion of dose-response area to be identified as labels for the gene.
nDoseInt	number of dose related breaks in the gene label's table. default is 3
nTimeInt	number of time related breaks in the gene label's table. default is 3
doseLabels	vector of colnames (doses) for the gene label's table. default is c("Sensitive","Intermediate","Resilient")
timeLabels	vector of rownames (time points) for the gene label's table. default c("Late","Middle","Early")
toPlot	it true the gene map is displayed
addLegend	if true the legend will be added to the plot
tosave	if true a png of the gene map is saved in path
path	path of the folder where to save the gene map
mode	is a character specifying when an area is called active. values can be "cumulative" or "presence". If presence, an area is called active if at least one of its pixel is on the BMD curve. If cumulative, the number of region needed to reach the th

an object of class TinderMIX containing the fitted BMD object, the IC50 value. The function plot the map showing the responsive region. This function identify the BMD area and the IC50 value in the time and dose maps

angy89/TinderMIX documentation built on Nov. 26, 2020, 9:26 p.m.