getManualCountsEstimates: FrenchFISH function for generating volume adjusted spot...

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

Description

FrenchFISH function for generating volume adjusted spot counts from spots which have been manually counted (uses a Markov chain Monte Carlo method). Returns five quantile estimates and the mean estimate.

Usage

getManualCountsEstimates(
  probeCounts,
  radius,
  height,
  volumeFracCorrection = "max"
)

Arguments

probeCounts	A matrix of manual spot counts with columns for probes and rows for nuclei
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 'max')

Value

The volume adjusted spot counts for each probe that have been generated using MCMC modelling

Examples

manualCountsEstimates<-getManualCountsEstimates(cbind(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.