Xpress: Xpress

In AndersenLab/easyXpress: A Package to Read, Process, and Analyze Worm Data Generated from CellProfiler’s WormToolbox

Xpress

Description

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.

AndersenLab/easyXpress documentation built on Dec. 6, 2024, 4:04 a.m.