| Title: | Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections |
|---|---|
| Description: | FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting. |
| Authors: | Adam Berman, Geoff Macintyre |
| Maintainer: | Adam Berman <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.17.0 |
| Built: | 2024-07-05 04:47:17 UTC |
| Source: | https://github.com/bioc/frenchFISH |
Helper function to check if all values in the input count matrix are either NA, NaN, or non-negative integers
areAllNonnegativeIntegers(count_matrix)areAllNonnegativeIntegers(count_matrix)
count_matrix |
The count matrix |
TRUE if all values in count_matrix are non-NA/NaN, non-negative integers; otherwise FALSE
Helper function to check the arguments input to getAutomaticCountsEstimates
checkAutomaticCountsEstimatesArguments(probeCounts, radius, height)checkAutomaticCountsEstimatesArguments(probeCounts, radius, height)
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 |
The cells' nuclear radius (must be measured in same unit as
|
height |
The section height (must be measured in same unit as
|
Nothing if all checks are passed; otherwise throws an error or warning message
Helper function to check the arguments input to getManualCountsEstimates
checkManualCountsEstimatesArguments(probeCounts, radius, height)checkManualCountsEstimatesArguments(probeCounts, radius, height)
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 |
The section height (must be measured in same unit as
|
Nothing if all checks are passed; otherwise throws an error or warning message
Function to convert CSV output of the FISHalyseR automatic FISH splot counting software to a count matrix suitable for input to frenchFISH's getAutomaticCountsEstimates
convertFishalyserCsvToCountMatrix(pathToFishalyserCsv)convertFishalyserCsvToCountMatrix(pathToFishalyserCsv)
pathToFishalyserCsv |
The path to the CSV file of automatic spot counts outputted by FISHalyseR |
A count matrix suitable for input to getAutomaticCountsEstimates
probeCounts<-convertFishalyserCsvToCountMatrix( system.file("extdata", "SampleFISH.jpg_data.csv", package="frenchFISH"))probeCounts<-convertFishalyserCsvToCountMatrix( system.file("extdata", "SampleFISH.jpg_data.csv", package="frenchFISH"))
Helper function to convert spot counts and nuclear area measurements into continuous events for Poisson point estimation
generatePPdat(area, spots)generatePPdat(area, spots)
area |
The nuclear area |
spots |
The number of spots counted |
Vector of continuous events for Poisson point estimation
FrenchFISH function for generating Poisson point estimates of spot counts from spot counts which have been automatically generated.
getAutomaticCountsEstimates(probeCounts, radius, height)getAutomaticCountsEstimates(probeCounts, radius, height)
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 |
The cells' nuclear radius (must be measured in same unit as
|
height |
The section height (must be measured in same unit as
|
The Poisson point estimates of spot counts for each probe
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)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)
Helper function to get the average volume of nucleus sampled given the nucleus radius and section height
getAverageVolumeFrac(r, h)getAverageVolumeFrac(r, h)
r |
The nuclear radius |
h |
The section height |
The average volume of nucleus sampled given the nucleus radius and section height
FrenchFISH function for generating volume adjusted spot counts from spots which have been manually counted (uses a Markov chain Monte Carlo method).
getManualCountsEstimates(probeCounts, radius, height)getManualCountsEstimates(probeCounts, radius, height)
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 |
The section height (must be measured in same unit as
|
The volume adjusted spot counts for each probe that have been generated using MCMC modelling
manualCountsEstimates<-getManualCountsEstimates(cbind(red=c(0,2,4), green=c(5,3,1), blue=c(3,0,2)), 8, 4)manualCountsEstimates<-getManualCountsEstimates(cbind(red=c(0,2,4), green=c(5,3,1), blue=c(3,0,2)), 8, 4)
Helper function to get the maximum possible volume of nucleus sampled given the nucleus radius and section height
getMaxVolumeFrac(r, h)getMaxVolumeFrac(r, h)
r |
The nuclear radius |
h |
The section height |
The maximum possible volume of nucleus sampled given the nucleus radius and section height
Helper function that returns the minimum possible volume of nucleus sampled given the nucleus radius and section height
getMinVolumeFrac(r, h)getMinVolumeFrac(r, h)
r |
The radius of the nuclei |
h |
The height of the section |
The minimum possible volume of nucleus sampled given the nucleus
Helper function that returns the fraction of the nucleus sampled for a specified distance from the midpoint
getVsegFrac(d, h, r)getVsegFrac(d, h, r)
d |
The distance sampled from the midpoint |
h |
The height of the section |
r |
The radius of the nuclei |
The fraction of the nucleus sampled for a specified distance from the midpoint