mIFTO: mIFTO: Multiplex Immunoflourescence Titration Optimization

Multiplex Immunoflouresence Titration Optimization (mIFTO) R Package - workflow

check values in the general input table for errors or mistakes
Slide_ID: check slide descriptors
- ERROR: check for empty
- WARNING: check for illegal characters '-|+|&'
- WARNING: check for and remove whitespace
- split at commas for different slide descriptors
Antibody: check antibody variable
- ERROR: check for empty
Concentration: check concentration variable
- ERROR: check for empty
- WARNING: check for and remove whitespace
- split at commas and convert to numeric values
- ERROR: on error, this indicates non-numeric values so exit
- ERROR: check if the list is not sorted or that any of the values are less than zero
Opal1: Fluorophore TSA valye
- ERROR: check for empty
Antibody_Opal: combine the Antibody and Opal1 variables with a space, put Opal1 in paraen.
- paste0(Antibody, '_(', Opal1, ')')
Evalutate the image\ folder names
- if naming convention is set to true
- titration.type.name variable is set to either Antibody, 'Primary Antibody' input, or Opal````, 'Fluorophore (TSA)' input, based on thetitration.type``` specified in the drop down menu 'What is being titrated?'
- The code will only search for concentrations following the titration.type.name
- if naming convention is set to false
- set the titration.type.name to blank
- this means it will search for the concentration in every part of the name

for the specified run type ('pixels','cells','tissue') extract the Vars variable (Vars_pixels, Vars_cells, Vars_tissue)
collapse the vars on commas and check the string for specifiers
flowout: output the flow-like csv results
decile.logical: output decile results
ihc.logical: an IHC was included in the analysis and should have results exported
m.folders: whether or not the data is in one folder or folders separated by dilution
threshold.logical: whether or not the data has defined thresholds

wd: choose the working directory
- ERROR: on selecting cancel
append the titration.type.name to the concentration as the search paths for data
- the search is set so that the slide name must either end with the concentration or have no additional 0s attached to the concentration
- ERROR: check that there is one and only one path for each concentration
check if the IHC value was indicated
- if the IHC is indicated check that at least one file of the specified data type is included for each slide