pipeline: pipeline with report generation

In Peyronlab/MACSQuantifyR: Fast treatment of MACSQuantify FACS data

Description

Loads user's data, prompt a graphical representation of a 96 well plate and let the user select where the duplicates of each condition were placed. Use for reordering excel file. Plate image with selection can also be saved in the form of a png file in the output_MQ directory.

Also generates a complete report with the graphics

Usage

pipeline(filepath,sheet_name=NULL,number_of_replicates,number_of_conditions,
control=FALSE,save.files=TRUE,MACSQuant.obj=NULL)

Arguments

filepath	path of the excel file
sheet_name	Name of the sheet to load (optional, first sheet is default)
number_of_replicates	For each condition, the number of duplicates (must be the same for all conditions)
number_of_conditions	The number of conditions tested (eg: Drug 1 alone, Drug 2 alone)
control	Is there a control in this experiment (eg: Staurosporin)
save.files	Used to save the image in the output folder
MACSQuant.obj	object of class MACSQuant

Value

A formatted report file along with intermediates results

Examples

print("run manually, requires user input")
filepath <- system.file("extdata", "SingleDrugs.xlsx",
    package = "MACSQuantifyR")
# pipeline(filepath,3,5)
# let you select 5 conditions of 3 replicates each

Peyronlab/MACSQuantifyR documentation built on April 4, 2020, 11:24 a.m.