run_all_BMD_IC50: This function run the compute_BMD_IC50 for all genes and...

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

Usage

run_all_BMD_IC50(contour_res, activity_threshold = 0.1,
  BMD_response_threshold = 0.95, nDoseInt = 3, nTimeInt = 3,
  doseLabels = c("Late", "Middle", "Early"),
  timeLabels = c("Sensitive", "Intermediate", "Resilient"),
  tosave = FALSE, toPlot = FALSE, addLegend = FALSE, path = ".",
  relGenes, mode = "cumulative")

Arguments

contour_res	object resulting from the create_contour function
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")
tosave	if true a png of the gene map is saved in path
path	path of the folder where to save the gene map
relGenes	vector of genes with signifincant pvalues from the fitting
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 \item coordmatrix with x and y coordinate. The first column contain the doses, while the second one the time points \item geneNameis a character string containing the gene name

a list with two object: Mat is a matrix with genes on the rows and labels on the columns. GeneRes is a list of results from the compute_BMD_IC50 function, one for every gene This function run the compute_BMD_IC50 for all genes and return a matrix with label associated to every gene

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