parameter1: Exclusion Criteria-1 of Neighborful Algorithm

In sathishsrinivasank/pinerrordetector: Detection of Pinning Errors of Robotic Machines used in SGA Yeast Screen

Description

Exclusion Criteria-1 used in neighborful algorithm on combinations of neighbors adjoining the selected colony. See help(neighborful_algorithm)

Usage

parameter1(colony, combinations, colony_area_raw_data, plate_median_threshold,
  excluded_colonies, param1_threshold)

Arguments

colony	selected colony by the outer loop of the neighborful algorithm
combinations	combinations of neighbors adjoining the selected colony
colony_area_raw_data	A numeric vector of raw data representing the area yeast grown at a specific location on a nutrient medium agar plate
plate_median_threshold	Threshold used in the plate median
excluded_colonies	A numeric vector of indices that are part of excluded colonies
param1_threshold	The numerical value which can be one from 1:8. This exclusion criteria-1 of neighborful algorithm represents the number of adjoining neighbors of the selected colony from colony that has colony area less than or equal to plate_median_threshold. If the selected colony is surrounded by at least param1_threshold neighbors, then it will be considered as excluded colony by the neighborful algorithm

Value

If the selected colony passes the exclusion criteria - 1, then a vector of excluded colonies with the selected colony will be returned. Else, it will return -1.

Examples

plateformat <- 1536
middle_colony <- 34
param1_threshold <- 6
neighbors_selected_colony <- middle_neighbors(plateformat, middle_colony)
combin_coords <- combn(length(neighbors_selected_colony), param1_threshold)
combinations <- neighbors_selected_colony[(combin_coords[,1])]
data_area <- simulated_data_1536(data_384 = colonyarea$data_subtypes,
                                 in_data_flow = "across",
                                 out_data_flow = "down",
                                 is_plate_coords = TRUE)
empty_indices <- which(convert_small_to_large(plate_from = 384,
                                              plate_to = 1536,
                                              data_from = colonyarea$data_subtypes,
                                              in_data_flow = 'across',
                                              out_data_flow = "down",
                                              is_plate_coords = FALSE)$y %in% 'Empty')
p_median <- plate_median(empty_indices = empty_indices,
                         colony_area_raw_data = data_area$y)
plate_median_threshold <- p_median/4
parameter1(colony = middle_colony,
           combinations = combinations,
           colony_area_raw_data = data_area$y,
           plate_median_threshold = plate_median_threshold,
           excluded_colonies = c(2),
           param1_threshold = param1_threshold)

sathishsrinivasank/pinerrordetector documentation built on May 7, 2019, 2:55 a.m.