new_class_MQ {MACSQuantifyR} | R Documentation

## 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)

[Package MACSQuantifyR version 1.1.2 Index]