append_data_frame {synapsis}R Documentation

append_data_frame

Description

applies new row to data frame

Usage

append_data_frame(
  WT_str,
  KO_str,
  WT_out,
  KO_out,
  img_file,
  foci_areas,
  df_cells,
  cell_count,
  stage,
  foci_per_cell,
  image_mat,
  percent_px,
  alone_foci,
  discrepant_category,
  C1
)

Arguments

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 -/-.

img_file

cell's file name

foci_areas

pixel area of each foci

df_cells

current data frame

cell_count

unique cell counter

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.

foci_per_cell

foci count for cell

image_mat

matrix with all pixel values above zero

percent_px

percentage of foci mask that coincides with strand channel small number indicates potentially problematic image.

alone_foci

estimated number of foci that are NOT on a strand.

discrepant_category

estimated number of foci that are NOT on a strand.

C1

criteria

Value

data frame with new row


[Package synapsis version 0.99.18 Index]