new_class_MQ: Create a new MACSQuant object

In Peyronlab/MACSQuantifyR: Fast treatment of MACSQuantify FACS data

Description

The user can create a new custom MACSQuant object This function is also used in internal code for MACSQuant initialization

Usage

#initialize empty MACSQuant object
new_class_MQ(my_data=NULL,my_data_sorted=NULL,my_replicates_sorted=NULL,
experiment_name=NULL,statistics=NULL,combination.index.df=NULL,
number_of_replicates=NULL,number_of_conditions=NULL,doses=NULL,
doses.alt=NULL,c_names=NULL, control=NULL,plt.title=NULL,
plt.labels=NULL,plt.col=NULL,save.files=NULL,path=tempdir())
#initialize custom MACSQuant object
new_class_MQ(my_data,my_data_sorted=NULL,my_replicates_sorted=NULL,
experiment_name=NULL,statistics=NULL,combination.index.df=NULL,
number_of_replicates=NULL,number_of_conditions=NULL,
doses=NULL,doses.alt=NULL, c_names=NULL,control=NULL,plt.title=NULL,
plt.labels=NULL,plt.col=NULL, save.files=NULL,path=tempdir())

Arguments

my_data	Contains the raw data
my_data_sorted	Contains the sorted data (according to replicates order)
my_replicates_sorted	Contains the sorted matrix containing replicates names
experiment_name	User defined experiment named. Used for the report generation
statistics	Contains the statistics for each condition
combination.index.df	data.frame that contains the outputs of the combination_index function
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)
doses	Numeric vector representing doses for each conditions
doses.alt	In case of interaction test second dose vector
c_names	Vector containing experiment names
control	logical: is there a control in this experiment (eg: Staurosporin)
plt.title	Title of the experiment to add to the barplot
plt.labels	legend labels for the bar plot
plt.col	color vector for the graphical representations
save.files	Used to save the image in the output folder
path	path of the experiment output folder (default '.')

Value

A formatted report file along with intermediates results

Examples

# initialize empty MACSQuant object
new_class_MQ()
# initialize custom MACSQuant object
my_data <- data.frame(character(length = 10), character(length = 10),
    numeric(length = 10), numeric(length = 10))
names(my_data) <- c("Full path", "WID", "%-#", "Count/mL")
new_class_MQ(my_data)

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