readData: Read data

In mknoll/cmoRe: Analysis of CellProfiler acquired data for disease profiling and drug discovery.

Read data

Description

Reads experiment associated data. Variables get suffix .cell, .nucl, .cyto

Usage

readData(
  data,
  vars = NULL,
  treatVar = c("Treatment", "Konzentration"),
  wellVar = "well",
  files = c("Treatment.csv", "Cells.txt", "Primarieswithoutborder.txt",
    "Cytoplasm.txt"),
  normalizeWells = T,
  sepTreat = "_",
  adaptVars = F,
  force = F,
  filterVars = c("Intensity_IntegratedIntensity_DNA", "Intensity_MedianIntensity_DNA",
    "AreaShape_Area")
)

Arguments

data	list contianing a lists of filesnames, all corresponding a separate experiment
vars	Variables to read, defaults to NULL (all variables)
treatVar	Treatment / Grouping variables as given in the treatment file
files	CellProfiler output files and treatment file
normalizeWells	convert A01->A1
force	force continuation if dimensions don't match
well	Well Variable within the treatment file

mknoll/cmoRe documentation built on Nov. 18, 2022, 4:01 p.m.