get_count_table: Get ScreenR count table

In EmanuelSoda/ScreenR: Package to Perform High Throughput Biological Screening

Get ScreenR count table

Description

Get function for the count table of the ScreenR object

Usage

get_count_table(object)

## S4 method for signature 'screenr_object'
get_count_table(object)

Arguments

object

The ScreenR object obtained using the create_screenr_object

Value

The count table of the ScreenR object

Slots

count_table

It is used to store the count table to perform the analysis

annotation_table

It is used to store the annotation of the shRNA

groups

It is used to store the vector of treated and untreated

replicates

It is used to store information about the replicates

normalized_count_table

It is used to store a normalized version of the count table

data_table

It is used to store a tidy format of the count table

Examples

object <- get0("object", envir = asNamespace("ScreenR"))
count_table <- get_count_table(object)
head(count_table)
data("count_table", package = "ScreenR")
data("annotation_table", package = "ScreenR")

groups <- factor(c(
    "T1/T2", "T1/T2", "Treated", "Treated", "Treated",
    "Control", "Control", "Control", "Treated", "Treated",
    "Treated", "Control", "Control", "Control"
))

obj <- create_screenr_object(
    table = count_table,
    annotation = annotation_table,
    groups = groups,
    replicates = c("")
)

EmanuelSoda/ScreenR documentation built on Sept. 29, 2023, 12:33 a.m.