Xpress

This is a wrapper function that will run all functions in the package and output a processed dataframe.

Usage

Xpress(
  filedir,
  rdafile,
  ...,
  design = FALSE,
  radius = 825,
  center_x = 1024,
  center_y = 1024,
  cluster_flag = TRUE,
  well_edge_flag = TRUE
)

Arguments

filedir

The project directory or directories with CellProfiler data. Provide a full path to the directory or a vector of project directory paths. Each directory must have a cellprofiler-nf output .rda file in a sub-folder named cp_data.

rdafile

The specific .rda file name in the cp_data directory to read. If multiple project directories are supplied to filedir, then include the .rda files for each project in the same order of the directories given in filedir.

...

specify variable used to summarize data. Variable names can be listed in succession.

design

Logical parameter, if TRUE then a design file will be joined to data. The design file should be located in a sub-folder of the filedir named design. If FALSE no design file will be joined.

radius

Radius in pixels away from image center with even illumination.

center_x

center x position of image

center_y

center y position of image

cluster_flag

Logical parameter; do you want worm objects in a cluster to be excluded when calculating well outliers? We recommend TRUE as the default.

well_edge_flag

Logical parameter; do you want worm objects in close proximity to the well edge to be excluded when calculating well outliers? We recommend TRUE as the default.

Value

List with four elements: raw data, processed data, and summaries for both datasets.