pipeline: pipeline with report generation

Description Usage Arguments Value Examples

View source: R/pipeline.R

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

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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

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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.