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

Description Usage Arguments Value Examples

View source: R/frenchfish.R

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

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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

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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.