neighborless_algorithm: Neighborless Algorithm

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

Description

Neighborless algorithm detects the pinning error of a plate by first excluding the empty indices and then checks for colony area. If the colony area is zero, then the algorithm concludes it as one of excluded colonies.

Usage

neighborless_algorithm(plateformat, colony_area_raw_data, empty_indices,
  excluded_colonies, is_save = FALSE, excluded_file = NULL)

Arguments

plateformat	An integer which can be one of 96 or 384 or 1536.
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. The data can be either rowwise or columnwise and its arrangement does not influence the outcome of this algorithm.
empty_indices	A numeric vector of indexed empty locations. It can also be the indices of control colonies grown on a plate, which may be used for normalizing the colony area of a plate
excluded_colonies	A numeric vector of indices that are part of excluded colonies
is_save	logical. If TRUE, then this function will save the list of excluded colonies obtained from neighborless algorithm as .RDS format in the specified excluded_file.
excluded_file	If is_save is TRUE, then the file name with full path for saving the list of excluded colonies must be specified.

Value

Invisible numeric vector of excluded colonies from neighborless algorithm.

Examples

plateformat <- 1536
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)$y %in% 'Empty')
(neighborless_algorithm(plateformat          = 1536,
                        colony_area_raw_data = data_area$y,
                        empty_indices        = empty_indices,
                        excluded_colonies    = c(),
                        is_save              = FALSE,
                        excluded_file        = NULL))

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