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

Description Usage Arguments Value Examples

View source: R/frenchfish.R

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

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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

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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.