new_class_MQ: Create a new MACSQuant object

Description Usage Arguments Value Examples

View source: R/new_class_MQ.R

Description

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

Usage

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#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

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# 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)

MACSQuantifyR documentation built on Nov. 8, 2020, 5:08 p.m.