Package 'MACSQuantifyR'

Generate barplots

Description

Uses the informations stored in the statistic tables of the MACSQuant object to generate barplots for the specified conditions. Plots can also be saved in the form of a png file in the output_MQ directory.

Usage

barplot_data(MACSQuant,plt.col=NULL,plt.conditions=NULL, plt.flavour=NULL,
plt.labels = NULL, plt.combo=FALSE,plt.3D.only = NULL,...)

Arguments

MACSQuant	object of class MACSQuant resulting of the function load_maxQuant(). Contains the original data table
plt.col	In case of manual run is used to define the bar colors. (must be the same for all conditions)
plt.conditions	user defined vector of conditions to plot (example: plt.conditions=c(1:9))
plt.flavour	Which barplot to produce, cell count or percentage of fluorochrome (i.e: "counts","percent")
plt.labels	xlabels of the plot
plt.combo	Does the experiment involves multiple variables (i.e some condition are a drug combination screening)
plt.3D.only	Whether to plot 3D barplot alone
...	params for lattice cloud namely z and x for parameter screen default for z and x are c(-110,-70) and argument xlab and ylab

Value

returns a barplot of the data

Examples

drugs_R_image <- system.file("extdata",
    "drugs.RDS",
    package = "MACSQuantifyR")
MACSQuant <- readRDS(drugs_R_image)
flavour <- "counts"
number_of_conditions <-
    slot(MACSQuant, "param.experiment")$number_of_conditions
plt.col <- c(rep(2, number_of_conditions), 1)
barplot_data(MACSQuant,
    plt.col = plt.col,
    plt.conditions = NULL,
    plt.flavour = flavour,
    plt.labels = NULL,
    plt.combo = FALSE)

---

compute combination index

Description

This function allows the user to compute combination index on the drug combinations. This function also generates intermediary plots and tables.

Usage

combination_index(MACSQuant, ...)

Arguments

MACSQuant	object of class MACSQuant resulting of the function load_maxQuant(). Contains the original data table
...	params for lattice cloud namely z and x for parameter screen default for z and x are c(-110,-70) and argument xlab and ylab

Value

Several plots and combination index

References

Chou, T. C. (2006). Theoretical basis, experimental design, and computerized simulation of synergism and antagonism in drug combination studies. Pharmacological reviews, 58(3), 621-681.

Examples

filepath <- system.file("extdata", "drugs.Rdata",
    package = "MACSQuantifyR")
load(filepath)
combination_index(MACSQuant)

---

Word report generation

Description

Allows the user to generate a report at every steps of the analysis

Also generates a complete report with the graphics

Usage

generate_report(MACSQuant)

Arguments

MACSQuant

object of class MACSQuant resulting of the function load_maxQuant(). Contains the original data table

Value

A formatted report

Examples

drugs_R_image <- system.file("extdata",
    "drugs.RDS",
    package = "MACSQuantifyR")
MACSQuant <- readRDS(drugs_R_image)
generate_report(MACSQuant)

---

Load xls file from maxQuant 96-well-plate device

Description

Load xls file from maxQuant 96-well-plate device

Usage

load_MACSQuant(filepath,sheet_name= NULL,MACSQuant.obj= NULL)

Arguments

filepath	path of the excel file
sheet_name	Name of the sheet to load (optional, first sheet is default)
MACSQuant.obj	object of class MACSQuant

Value

An object called MACSQuant of class MACSQuant containing variable my_data that corresponds to the data of the excel file in R

Examples

filepath <- system.file("extdata", "SingleDrugs.xlsx",
    package = "MACSQuantifyR")
# load_MACSQuant(filepath)

---

The MACSQuant Class

Description

MACSQuant object contains all the data and the user parameters

Slots

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

Contains the experiment name given by the user

statistics

Contains the statistics for each condition

combination.index.df

data.frame that contains the outputs of the combination_index function

param.experiment

list that contains the parameters relative to the experiment (i.e, number of replicates, number of conditions...)

param.output

List that contains the parameters relative to the report generation and outputs (i.e, save intermediary results, generate full report..)

---

Create a new MACSQuant object

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)

---

Sort experimental design on graphical 96-well-plate

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 "specified_path/output_MQ" directory.

Usage

on_plate_selection(MACSQuant,number_of_replicates,number_of_conditions,
control=FALSE,save.files=FALSE)

Arguments

MACSQuant	object of class MACSQuant resulting of the function load_maxQuant(). Contains the original data table
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

Value

A formatted report file along with intermediates results

Examples

print("run manually, requires user input")
# on_plate_selection(MACSQuant,3,5)
# let you select 5 conditions of 3 replicates each

---

pipeline with report generation

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

---

accessor function to access raw data

Description

This function allows the user to access raw data table

Usage

rData(MACSQuant)

Arguments

MACSQuant

object of class MACSQuant resulting of the function load_maxQuant(). Contains the original data table

Value

the raw data table

Examples

filepath <- system.file("extdata", "SingleDrugs.xlsx",
    package = "MACSQuantifyR")
#MACSQuant = load_MACSQuant(filepath)

#rData(MACSQuant)

---

sets custom output path

Description

This function allows the user to set the output directory path

Usage

setPath(MACSQuant,path=NULL)

Arguments

MACSQuant	object of class MACSQuant resulting of the function load_maxQuant(). Contains the original data table
path	user defined path, default is tempd

Value

object of class MACSQuant with updated path

Examples

filepath <- system.file("extdata", "SingleDrugs.xlsx",
    package = "MACSQuantifyR")
#MACSQuant = load_MACSQuant(filepath)
user_path="."
#MACSQuant = setPath(MACSQuant,path=user_path)

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accessor function to access sorted data

Description

This function allows the user to access sorted data table

Usage

sorted(MACSQuant)

Arguments

MACSQuant

object of class MACSQuant resulting of the function load_maxQuant(). Contains the original data table

Value

the raw data table

Examples

filepath <- system.file("extdata", "SingleDrugs.xlsx",
    package = "MACSQuantifyR")
#MACSQuant = load_MACSQuant(filepath)

#sorted(MACSQuant)

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