getAutomaticCountsEstimates: FrenchFISH function for generating Poisson point estimates of...

In markowetzlab/frenchFISH: Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections

Description

FrenchFISH function for generating Poisson point estimates of spot counts from spot counts which have been automatically generated. Returns a low confidence interval, a median, and a high confidence interval estimate.

Usage

getAutomaticCountsEstimates(
  probeCounts,
  radius,
  height,
  volumeFracCorrection = "avg"
)

Arguments

probeCounts	A matrix where the first column contains the areas of the nuclear blobs (this column must be named "area" and the unit of its entries must be the square of the unit used to measure radius and height) and the remaining columns (one per probe) contain the spot counts for different probes in each nuclear blob
radius	The cells' nuclear radius (must be measured in same unit as height)
height	The section height (must be measured in same unit as radius)
volumeFracCorrection	The method used to correct for volume fraction (must be 'avg', 'max', or 'min'; defaults to 'avg')

Value

The Poisson point estimates of spot counts for each probe

Examples

automaticCountsEstimates<-getAutomaticCountsEstimates(
    cbind(area=c(250,300,450), 
    red=c(0,2,4), 
    green=c(5,3,1), 
    blue=c(3,0,2)), 8, 4)

markowetzlab/frenchFISH documentation built on June 28, 2020, 8:18 p.m.