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
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
#> An object of class "screenr_object"
#> Slot "count_table":
#> # A tibble: 4 × 5
#> Barcode Time_3_rep1 Time_3_rep2 Time_3_TRT_rep1 Time_3_TRT_rep2
#> <chr> <chr> <chr> <chr> <chr>
#> 1 Code_1 3520 3500 1200 1250
#> 2 Code_2 3020 3000 1100 1000
#> 3 Code_3 1507 1457 1300 1400
#> 4 Code_3 1400 1490 1350 1375
#>
#> Slot "annotation_table":
#> # A tibble: 4 × 5
#> Gene Barcode Gene_ID Sequence Library
#> <chr> <chr> <lgl> <lgl> <lgl>
#> 1 Gene_1 Code_1 NA NA NA
#> 2 Gene_1 Code_2 NA NA NA
#> 3 Code_2 Code_3 NA NA NA
#> 4 Code_2 Code_3 NA NA NA
#>
#> Slot "groups":
#> [1] Control Control Treated Treated
#> Levels: Control Treated
#>
#> Slot "replicates":
#> [1] ""
#>
#> Slot "normalized_count_table":
#> # A tibble: 0 × 0
#>
#> Slot "data_table":
#> # A tibble: 0 × 0
#>