populate.tables: Used to loop through each image, call the generate func and...
In AstroPathJHU/mIFTO: mIFTO: Multiplex Immunoflourescence Titration Optimization

populate.tables

R Documentation

Used to loop through each image, call the generate func and map back to Tables; Created By: Benjamin Green; Last Edited 05/29/2020

Description

This function is desgined to do analysis for IF titration series in Pixel by Pixel data provding output for each IMAGE individually grouped by Concentration

Usage

populate.tables(
  Slide_Descript,
  Concentration,
  Antibody_Opal,
  Thresholds,
  Opal1,
  flowout,
  Protocol,
  paths,
  titration.type.name,
  connected.pixels,
  decile.logical,
  threshold.logical,
  pb.count,
  pb.Object
)

Arguments

`Concentration`	a numeric vector of concentrations used in the titration
`Antibody_Opal`	the paired string for an antibody opal pair, designated as "AB (Opal NNN)"
`Thresholds`	a list of thresholds used for each concentration and slide
`Opal1`	the opal value of interest
`flowout`	logical for whether or not flow like results will be produced (1 for produce, 0 for don't)
`Protocol`	the protocol type (7color or 9color)
`paths`	the data paths, one data path for each concentration
`titration.type.name`	the titration type for a given dilution set (Primary or TSA)
`connected.pixels`	the number of pixels that a pixel must be connected to for positivity measures
`decile.logical`	whether or not to run a decile approach analysis
`threshold.logical`	whether or not to run a threshold approach analysis
`pb.count`	current count for progress bar
`pb.Object`	progress bar object
`Slide_Desctipt`	a unique identifier for each slide to be analyzed