get_coincident_foci: get_coincident_foci

In mcneilllucy/synapsis: An R package to automate the analysis of double-strand break repair during meiosis

Description

calculates the statistic to compare to crisp_criteria, which determines whether the foci count will be reliable

Usage

get_coincident_foci(
  offset_px,
  offset_factor,
  brush_size,
  brush_sigma,
  annotation,
  watershed_stop,
  watershed_radius,
  watershed_tol,
  crowded_foci,
  artificial_amp_factor,
  strand_amp,
  disc_size,
  disc_size_foci,
  img_file,
  cell_count,
  img_orig,
  img_orig_foci,
  stage,
  WT_str,
  KO_str,
  WT_out,
  KO_out,
  C1_search,
  discrepant_category,
  C1,
  C2,
  df_cells,
  C_weigh_foci_number
)

Arguments

offset_px,	Pixel value offset used in thresholding of synaptonemal complex channel
offset_factor,	Pixel value offset used in thresholding of foci channel
brush_size,	size of brush to smooth the foci channel. Should be small to avoid erasing foci.
brush_sigma,	sigma for Gaussian smooth of foci channel. Should be small to avoid erasing foci.
annotation,	Choice to output pipeline choices (recommended to knit)
watershed_stop	Stop default watershed method with "on"
watershed_radius	Radius (ext variable) in watershed method used in foci channel. Defaults to 1 (small)
watershed_tol	Intensity tolerance for watershed method. Defaults to 0.05.
crowded_foci	TRUE or FALSE, defaults to FALSE. Set to TRUE if you have foci > 100 or so.
artificial_amp_factor	Amplification of foci channel, for annotation only.
strand_amp	multiplication of strand channel to make masks
disc_size	size of disc for local background calculation in synaptonemal complex channel
disc_size_foci	size of disc for local background calculation in foci channel
img_file	cell's file name
cell_count	unique cell counter
img_orig	original strand crop
img_orig_foci	cropped foci channel
stage,	meiosis stage of interest. Currently count_foci determines this with thresholding/ object properties in the synaptonemal complex channel by previosly calling the get_pachytene function. Note that if using this option, the count_foci function requires that the input directory contains a folder called “pachytene” with the crops in it.
WT_str	string in filename corresponding to wildtype genotype. Defaults to ++.
KO_str	string in filename corresponding to knockout genotype. Defaults to –.
WT_out	string in output csv in genotype column, for knockout. Defaults to +/+.
KO_out	string in output csv in genotype column, for knockout. Defaults to -/-.
C1_search	TRUE or FALSE whether the image is still being modified until it meets the crispness criteria
discrepant_category	estimated number of foci that are NOT on a strand.
C1	Default crispness criteria = sd(foci_area)/(mean(foci_area)+1)
C2	Alternative crisp criteria.
df_cells	current data frame
C_weigh_foci_number	choose crispness criteria- defaults to TRUE to use C1 (weighing with number). Otherwise set to FALSE to use C2

Value

data frame with new row with most recent foci per cell appended

mcneilllucy/synapsis documentation built on Dec. 21, 2021, 3:59 p.m.