cellAggregator: cellAggregator

In shazanfar/cellAggregator: Network simulation of cell-cell aggregation assays

Description

the cellAggregator function

Usage

cellAggregator(numCells, numProtsPerCell, bindingAffinity, timesteps = 100,
  burnIn = 0.75, verbose = TRUE, includeListOfGraphs = TRUE,
  plot = FALSE, ...)

Arguments

numCells	vector of the number of cells per cell population
numProtsPerCell	matrix (number of cell populations x number of protein types) specifying number of proteins per cell
bindingAffinity	matrix of binding affinities between proteins (should be symmetric matrix)
timesteps	(default 100) number of timesteps
burnIn	(default 0.75) consider the last burnIn proportion of timesteps for index calculation
verbose	(default TRUE) print messages
includeListOfGraphs	(default TRUE) include list of graphs in results object
plot	(default FALSE) if TRUE prints a breakdown of the input parameters
...	arguments go to bindProteins()
cellGraph	is an igraph object specifying the cell-cell bindings (only one of proteinGraph or cellGraph should be specified)

Value

list cellAggregationResult object containing the input parameters: numCells, numProtsPerCell, bindingAffinity, timesteps, burnIn, verbose, includeListOfGraphs; and output objects: listofCellGraphs (list of cell graphs per timestep), listofProteinGraphs (list of protein graphs per timestep), listoftIndex (list of t index per timestep), listofTabulation (list of tabulation of proteins per timestep), and t_index (final t index summary value across entire simulation).

Examples

numCells = c(25,25)
numProtsPerCell = rbind(c(5,0,0),c(5,5,5))
bindingAffinity = cbind(c(1,0,0), c(0,1,0), c(0,0,1))

cellAggregationResult = cellAggregator(
 numCells,
 numProtsPerCell,
 bindingAffinity,
 timesteps = 100,
 burnIn = 0.75,
 verbose = TRUE,
 includeListOfGraphs = TRUE,
 plot = TRUE
)

cellAggregationResult$t_index
unlist(cellAggregationResult$listoftIndex)
cellAggregationBarplot(cellAggregationResult)

shazanfar/cellAggregator documentation built on May 14, 2019, 7:35 a.m.