Set function for the annotation table of the ScreenR object
Usage
set_annotation_table(object, annotation_table)
# S4 method for screenr_object
set_annotation_table(object, annotation_table)Arguments
- object
The ScreenR object obtained using the
create_screenr_object- annotation_table
a table containing the annotation for each shRNA
Examples
object <- get0("object", envir = asNamespace("ScreenR"))
annotation <- get_annotation_table(object)
#> ScreenR annotation table containing:
#> 5320 rows
#> 5 columns
set_annotation_table(object, annotation)
#> An object of class "screenr_object"
#> Slot "count_table":
#> # A tibble: 5,320 × 15
#> Barcode T1 T2 Time3_TRT_A Time3_TRT_B Time3_TRT_C Time3_A Time3_B
#> <fct> <int> <int> <int> <int> <int> <int> <int>
#> 1 10208 3520 4283 2493 3998 3018 3393 3829
#> 2 10502 280 339 140 542 162 468 157
#> 3 10796 1507 1533 1120 1125 1286 1136 1095
#> 4 11089 3797 4151 2296 3857 3645 3677 3124
#> 5 11382 717 644 564 336 256 554 590
#> 6 11675 7330 7593 4927 6211 6504 7781 7183
#> 7 11969 4854 5371 4251 4921 5424 4627 3952
#> 8 12263 1539 1171 764 1258 923 1503 1150
#> 9 12555 4328 4051 3130 4720 4697 3870 3835
#> 10 12847 466 417 206 318 288 328 185
#> # ℹ 5,310 more rows
#> # ℹ 7 more variables: Time3_C <int>, Time4_TRT_A <int>, Time4_TRT_B <int>,
#> # Time4_TRT_C <int>, Time4_A <int>, Time4_B <int>, Time4_c <int>
#>
#> Slot "annotation_table":
#> # A tibble: 5,320 × 5
#> Gene Barcode Gene_ID Sequence Library
#> <chr> <fct> <lgl> <lgl> <lgl>
#> 1 Gene_380 10208 NA NA NA
#> 2 Gene_380 10502 NA NA NA
#> 3 Gene_380 10796 NA NA NA
#> 4 Gene_380 11089 NA NA NA
#> 5 Gene_380 11382 NA NA NA
#> 6 Gene_380 11675 NA NA NA
#> 7 Gene_380 11969 NA NA NA
#> 8 Gene_380 12263 NA NA NA
#> 9 Gene_380 12555 NA NA NA
#> 10 Gene_380 12847 NA NA NA
#> # ℹ 5,310 more rows
#>
#> Slot "groups":
#> [1] T1/T2 T1/T2 Treated Treated Treated Control Control Control Treated
#> [10] Treated Treated Control Control Control
#> Levels: Control T1/T2 Treated
#>
#> Slot "replicates":
#> [1] ""
#>
#> Slot "normalized_count_table":
#> # A tibble: 5,320 × 15
#> Barcode T1 T2 Time3_TRT_A Time3_TRT_B Time3_TRT_C Time3_A Time3_B
#> <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 10208 330. 437. 365. 439. 311. 358. 425.
#> 2 10502 26.2 34.6 20.5 59.5 16.7 49.3 17.4
#> 3 10796 141. 156. 164. 124. 132. 120. 121.
#> 4 11089 356. 424. 336. 424. 375. 388. 346.
#> 5 11382 67.2 65.7 82.6 36.9 26.3 58.4 65.4
#> 6 11675 687. 775. 722. 682. 669. 820. 797.
#> 7 11969 455. 548. 623. 540. 558. 488. 438.
#> 8 12263 144. 119. 112. 138. 95.0 158. 128.
#> 9 12555 406. 413. 459. 518. 483. 408. 425.
#> 10 12847 43.7 42.6 30.2 34.9 29.6 34.6 20.5
#> # ℹ 5,310 more rows
#> # ℹ 7 more variables: Time3_C <dbl>, Time4_TRT_A <dbl>, Time4_TRT_B <dbl>,
#> # Time4_TRT_C <dbl>, Time4_A <dbl>, Time4_B <dbl>, Time4_c <dbl>
#>
#> Slot "data_table":
#> # A tibble: 74,480 × 9
#> Barcode Gene Sample Frequency Sequence Library Gene_ID Day Treatment
#> <fct> <chr> <fct> <dbl> <lgl> <lgl> <lgl> <chr> <chr>
#> 1 10208 Gene_380 T1 330. NA NA NA T1 T1
#> 2 10208 Gene_380 T2 437. NA NA NA T2 T2
#> 3 10208 Gene_380 Time3_TR… 365. NA NA NA Time3 TRT
#> 4 10208 Gene_380 Time3_TR… 439. NA NA NA Time3 TRT
#> 5 10208 Gene_380 Time3_TR… 311. NA NA NA Time3 TRT
#> 6 10208 Gene_380 Time3_A 358. NA NA NA Time3 Time3
#> 7 10208 Gene_380 Time3_B 425. NA NA NA Time3 Time3
#> 8 10208 Gene_380 Time3_C 363. NA NA NA Time3 Time3
#> 9 10208 Gene_380 Time4_TR… 323. NA NA NA Time4 TRT
#> 10 10208 Gene_380 Time4_TR… 382. NA NA NA Time4 TRT
#> # ℹ 74,470 more rows
#>