create_screenr_object: Create the ScreenR Object

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

Create the ScreenR Object

Description

Initial function to create the Screen Object.

Usage

create_screenr_object(
  table = NULL,
  annotation = NULL,
  groups = NULL,
  replicates = c("")
)

Arguments

table	The count table obtained from the read alignment that contains the Barcodes as rows and samples as columns.
annotation	The annotation table containing the information for each Barcode and the association to the corresponding Gene
groups	A factor containing the experimental design label
replicates	A vector containing the replicates label

Value

An object containing all the needed information for the analysis.

Examples

count_table <-
    data.frame(
        Barcode = c("Code_1", "Code_2", "Code_3", "Code_3"),
        Time_3_rep1 = c("3520", "3020", "1507", "1400"),
        Time_3_rep2 = c("3500", "3000", "1457", "1490"),
        Time_3_TRT_rep1 = c("1200", "1100", "1300", "1350"),
        Time_3_TRT_rep2 = c("1250", "1000", "1400", "1375")
    )
annotation_table <-
    data.frame(
        Gene = c("Gene_1", "Gene_1", "Code_2", "Code_2"),
        Barcode = c("Code_1", "Code_2", "Code_3", "Code_3"),
        Gene_ID = rep(NA, 4), Sequence = rep(NA, 4),
        Library = rep(NA, 4)
    )

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

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